Variant report

Variant	rs1678537
Chromosome Location	chr12:57900341-57900342
allele	A/G
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	POLR2A	chr12:57899783-57900365	K562	blood:	n/a	n/a
2	POLR2A	chr12:57899954-57900341	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:57899586-57900462	K562	blood:	n/a	n/a
4	POLR2A	chr12:57900253-57900381	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57896366..57901111-chr12:57901647..57907518,8	K562	blood:
2	chr12:57889575..57891474-chr12:57898819..57900365,2	MCF-7	breast:
3	chr12:57889487..57901620-chr12:57907600..57919310,30	K562	blood:

Variant related genes	Relation type
RNU6-594P	TF binding region
ENSG00000252865	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000175197	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1148553	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1148554	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1148555	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1148557	0.91[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1284465	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1284605	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1284606	0.85[AMR][1000 genomes]
rs1299737	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1629410	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1669294	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1669296	0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1669297	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1709871	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1709874	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2127318	0.92[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs2620677	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2620679	0.92[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs2672571	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs2673326	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2928382	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2943696	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3782129	0.84[EUR][1000 genomes]
rs3847699	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs472895	0.88[AMR][1000 genomes]
rs474544	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760273	0.94[EUR][1000 genomes]
rs496245	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508904	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs511752	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs542278	0.91[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs569251	0.88[AMR][1000 genomes]
rs697221	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs703835	0.92[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs703836	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs703837	0.92[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs703838	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs703839	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7299631	0.84[EUR][1000 genomes]
rs747340	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs775236	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs775237	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs775241	0.92[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs775323	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775324	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs776038	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs776039	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7964074	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs796546	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7969683	0.93[EUR][1000 genomes]
rs899653	0.83[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs9737891	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
2	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
4	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
9	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
10	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers 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 miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
12	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
14	nsv899120	chr12:57886609-57921188	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1678537	CALCOCO1	cis	cerebellum	SCAN
rs1678537	AVIL	cis	cerebellum	SCAN
rs1678537	ITGA7	cis	cerebellum	SCAN
rs1678537	ACVRL1	cis	cerebellum	SCAN
rs1678537	STAT6	cis	parietal	SCAN
rs1678537	DCTN2	cis	Muscle Skeletal	GTEx
rs1678537	KRT7	cis	cerebellum	SCAN
rs1678537	ATF7	cis	cerebellum	SCAN
rs1678537	RDH5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57882800-57905800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:57883000-57910600	Weak transcription	Right Atrium	heart
3	chr12:57883200-57900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:57883200-57900600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:57883200-57900800	Strong transcription	Thymus	Thymus
6	chr12:57883200-57902400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:57883200-57911200	Strong transcription	Fetal Intestine Small	intestine
8	chr12:57883400-57900600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr12:57883400-57900600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:57883400-57900600	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:57883400-57900600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:57883400-57900600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:57883400-57900600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:57883400-57900800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:57883400-57903000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:57884000-57900600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:57884000-57900600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:57884000-57902400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:57884000-57903200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:57884400-57900800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:57885600-57911200	Weak transcription	Fetal Heart	heart
22	chr12:57887200-57900600	Strong transcription	Dnd41	blood
23	chr12:57887800-57900600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:57887800-57900600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:57888000-57900600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:57888000-57900600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:57888000-57900600	Strong transcription	Fetal Muscle Leg	muscle
28	chr12:57888600-57912200	Strong transcription	Fetal Stomach	stomach
29	chr12:57888800-57900600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:57888800-57900600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:57888800-57900600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:57889200-57900600	Strong transcription	Placenta	Placenta
33	chr12:57889400-57900600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:57889600-57900600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:57889600-57900600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:57889600-57900600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:57889800-57900600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:57889800-57900600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:57889800-57900600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr12:57889800-57900600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:57889800-57900600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:57889800-57900600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr12:57889800-57900600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr12:57889800-57900600	Strong transcription	Fetal Thymus	thymus
45	chr12:57889800-57900600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:57889800-57900600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr12:57889800-57900600	Strong transcription	Osteobl	bone
48	chr12:57890000-57900600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:57890200-57900600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:57890200-57900600	Strong transcription	Liver	Liver

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