Variant report

Variant	rs7308997
Chromosome Location	chr12:8148340-8148341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:8147523-8148379	HCT-116	colon:	n/a	chr12:8147995-8148008 chr12:8147996-8148006 chr12:8147988-8148009 chr12:8147993-8148011 chr12:8147999-8148008 chr12:8147994-8148010
2	CTCF	chr12:8147187-8148464	SK-N-SH	brain:	n/a	chr12:8147995-8148008 chr12:8147996-8148006 chr12:8147988-8148009 chr12:8147993-8148011 chr12:8147999-8148008 chr12:8147994-8148010
3	CHD1	chr12:8147793-8148353	GM12878	blood:	n/a	n/a
4	RAD21	chr12:8147215-8148575	IMR90	lung:	n/a	chr12:8147995-8148009 chr12:8147993-8148005 chr12:8147994-8148007 chr12:8147991-8148010 chr12:8147995-8148005 chr12:8148000-8148009
5	SPI1	chr12:8147708-8148354	GM12891	blood:	n/a	chr12:8147940-8147953 chr12:8147937-8147946 chr12:8148110-8148119
6	CTCF	chr12:8148240-8148390	SK-N-SH_RA	brain:	n/a	n/a
7	CTCF	chr12:8147019-8148491	A549	lung:	n/a	chr12:8147995-8148008 chr12:8147996-8148006 chr12:8147988-8148009 chr12:8147993-8148011 chr12:8147999-8148008 chr12:8147994-8148010
8	SMC3	chr12:8147186-8148633	SK-N-SH	brain:	n/a	chr12:8147995-8148005 chr12:8148002-8148009 chr12:8147995-8148009
9	RAD21	chr12:8147706-8148353	A549	lung:	n/a	chr12:8147995-8148009 chr12:8147993-8148005 chr12:8147994-8148007 chr12:8147991-8148010 chr12:8147995-8148005 chr12:8148000-8148009
10	SPI1	chr12:8147433-8148521	GM12878	blood:	n/a	chr12:8147940-8147953 chr12:8147937-8147946 chr12:8148110-8148119
11	RAD21	chr12:8147205-8148475	SK-N-SH	brain:	n/a	chr12:8147995-8148009 chr12:8147993-8148005 chr12:8147994-8148007 chr12:8147991-8148010 chr12:8147995-8148005 chr12:8148000-8148009
12	MXI1	chr12:8147146-8148752	IMR90	lung:	n/a	n/a
13	PBX3	chr12:8148333-8148682	SK-N-SH	brain:	n/a	n/a
14	PBX3	chr12:8148214-8148685	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr12:8148275-8148562	SK-N-SH	brain:	n/a	n/a
16	MAFK	chr12:8147921-8148544	IMR90	lung:	n/a	chr12:8148285-8148296
17	GATA3	chr12:8148086-8148622	SK-N-SH	brain:	n/a	chr12:8148112-8148122
18	POLR2A	chr12:8147176-8148729	U87	brain:	n/a	n/a
19	SMC3	chr12:8147550-8148341	GM12878	blood:	n/a	chr12:8147995-8148005 chr12:8148002-8148009 chr12:8147995-8148009
20	SPI1	chr12:8147910-8148350	HL-60	blood:	n/a	chr12:8147940-8147953 chr12:8147937-8147946 chr12:8148110-8148119
21	POLR2A	chr12:8147925-8148625	U87	brain:	n/a	n/a
22	SIN3A	chr12:8147782-8148359	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr12:8147925-8148624	U87	brain:	n/a	n/a
24	RCOR1	chr12:8147753-8148379	GM12878	blood:	n/a	n/a
25	CEBPB	chr12:8147887-8148556	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:8087187..8090473-chr12:8145986..8149446,6	K562	blood:
2	chr12:8086230..8090473-chr12:8145838..8149446,6	K562	blood:

Variant related genes	Relation type
ENSG00000240739	TF binding region
ENSG00000059804	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10732571	1.00[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10846306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846331	0.92[EUR][1000 genomes]
rs10846333	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10846366	0.85[EUR][1000 genomes]
rs11056818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35297839	0.81[CEU][hapmap]
rs4301853	0.98[EUR][1000 genomes]
rs4883465	0.85[ASN][1000 genomes]
rs4883470	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4883475	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4883476	0.81[EUR][1000 genomes]
rs58279638	0.89[EUR][1000 genomes]
rs6488819	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6488820	0.98[EUR][1000 genomes]
rs7138450	0.82[EUR][1000 genomes]
rs7139118	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7295576	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7299161	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7299583	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7303600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303774	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7304465	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957980	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7958000	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs7958511	0.94[EUR][1000 genomes]
rs7962349	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7962925	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7963223	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7974225	0.85[EUR][1000 genomes]
rs7974660	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048545	chr12:7778760-8608231	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv541368	chr12:7778760-8608231	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	esv1795892	chr12:7856819-8508693	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2758292	chr12:7856819-8623987	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	esv2759877	chr12:7856819-8623987	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv428270	chr12:7856819-8623987	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
7	nsv1054331	chr12:7924713-8183422	Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	esv1793008	chr12:7981374-8161231	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1797934	chr12:7985460-8214261	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv1793572	chr12:7995827-8568422	Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
11	esv1792916	chr12:8000336-8171838	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv469082	chr12:8000336-8171838	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv469084	chr12:8000336-8171838	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv469085	chr12:8000336-8171838	Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
15	nsv469086	chr12:8000336-8171838	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
16	nsv557298	chr12:8000336-8171838	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv541384	chr12:8003214-8188846	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
18	nsv1040972	chr12:8003413-8266291	Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
19	nsv541388	chr12:8003413-8266291	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
20	nsv916941	chr12:8003501-8608220	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
21	esv2751118	chr12:8017473-8190206	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
22	esv2754825	chr12:8024363-8167542	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
23	nsv869752	chr12:8026388-8174912	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
24	nsv898729	chr12:8044997-8190206	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
25	nsv1045521	chr12:8123225-8242846	Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
26	nsv898732	chr12:8123306-8190206	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
27	nsv1044509	chr12:8130958-8182060	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7308997	C12orf53	cis	cerebellum	SCAN
rs7308997	CLEC2D	cis	parietal	SCAN
rs7308997	GDF3	cis	cerebellum	SCAN
rs7308997	CLEC4D	cis	parietal	SCAN
rs7308997	PRB4	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8145800-8148400	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr12:8146000-8148400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr12:8146000-8148400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:8146000-8148400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:8146600-8148400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr12:8146600-8148400	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:8146800-8148400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:8147000-8148400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr12:8147000-8148400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:8147000-8148600	Enhancers	HMEC	breast
11	chr12:8147200-8148400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr12:8147200-8148400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr12:8147200-8148400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr12:8147200-8148400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:8147200-8148400	Enhancers	HSMM	muscle
16	chr12:8147200-8148600	Enhancers	Primary B cells from cord blood	blood
17	chr12:8147200-8148600	Enhancers	Primary B cells from peripheral blood	blood
18	chr12:8147200-8148600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:8147200-8148600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:8147400-8148400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:8147400-8148400	Enhancers	Hela-S3	cervix
22	chr12:8147400-8148600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:8147400-8148600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:8147400-8148600	Enhancers	Dnd41	blood
25	chr12:8147400-8148600	Enhancers	GM12878-XiMat	blood
26	chr12:8147600-8148400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:8147600-8148400	Enhancers	Primary T cells from cord blood	blood
28	chr12:8147600-8148400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:8147600-8148400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:8147600-8148400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:8147600-8148400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:8147600-8148400	Enhancers	Fetal Thymus	thymus
33	chr12:8147600-8148400	Flanking Active TSS	Osteobl	bone
34	chr12:8147600-8148600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr12:8147600-8148600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr12:8147600-8148600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:8147600-8148600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr12:8147600-8148600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:8147600-8148600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:8147800-8148400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:8147800-8148400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr12:8147800-8149000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:8148000-8148400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:8148000-8148400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:8148000-8148400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:8148000-8148400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:8148000-8148400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:8148000-8148400	Enhancers	Fetal Brain Female	brain
49	chr12:8148000-8148400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr12:8148000-8148400	Flanking Active TSS	NHDF-Ad	bronchial

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