Variant report

Variant	rs12316458
Chromosome Location	chr12:8231270-8231271
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	CTCF	chr12:8231120-8231270	GM12871	blood:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
2	RAD21	chr12:8230958-8231311	GM12878	blood:	n/a	chr12:8231157-8231176
3	RAD21	chr12:8230869-8231288	A549	lung:	n/a	chr12:8231157-8231176
4	CTCF	chr12:8231120-8231270	HCM	heart:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
5	CTCF	chr12:8230811-8231434	HCT-116	colon:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
6	ZNF384	chr12:8231021-8231324	K562	blood:	n/a	n/a
7	RAD21	chr12:8230975-8231273	MCF-7	breast:	n/a	chr12:8231157-8231176
8	RAD21	chr12:8230940-8231286	ECC-1	luminal epithelium:	n/a	chr12:8231157-8231176
9	RAD21	chr12:8230787-8231403	HCT-116	colon:	n/a	chr12:8231157-8231176
10	RAD21	chr12:8230969-8231340	HepG2	liver:	n/a	chr12:8231157-8231176
11	CTCF	chr12:8230956-8231346	GM12878	blood:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
12	CTCF	chr12:8230976-8231425	HCT-116	colon:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
13	CTCF	chr12:8231010-8231318	H1-hESC	embryonic stem cell:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
14	ZNF384	chr12:8230840-8231322	GM12878	blood:	n/a	n/a
15	SMC3	chr12:8230984-8231288	GM12878	blood:	n/a	chr12:8231161-8231175
16	RAD21	chr12:8230980-8231285	A549	lung:	n/a	chr12:8231157-8231176
17	CTCF	chr12:8231018-8231317	A549	lung:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
18	CTCF	chr12:8231120-8231270	NHEK	skin:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
19	RAD21	chr12:8230817-8231354	HCT-116	colon:	n/a	chr12:8231157-8231176
20	SMC3	chr12:8230955-8231331	Hela-S3	cervix:	n/a	chr12:8231161-8231175
21	RAD21	chr12:8230890-8231346	SK-N-SH_RA	brain:	n/a	chr12:8231157-8231176
22	RAD21	chr12:8230902-8231379	ECC-1	luminal epithelium:	n/a	chr12:8231157-8231176
23	CTCF	chr12:8230970-8231361	K562	blood:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
24	RAD21	chr12:8230918-8231352	H1-hESC	embryonic stem cell:	n/a	chr12:8231157-8231176
25	RAD21	chr12:8230901-8231348	IMR90	lung:	n/a	chr12:8231157-8231176
26	CTCF	chr12:8231120-8231270	NHDF-neo	bronchial:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
27	RAD21	chr12:8230961-8231295	SK-N-SH_RA	brain:	n/a	chr12:8231157-8231176
28	CTCF	chr12:8230911-8231277	A549	lung:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
29	RAD21	chr12:8230952-8231334	H1-hESC	embryonic stem cell:	n/a	chr12:8231157-8231176
30	ARID3A	chr12:8231015-8231318	K562	blood:	n/a	n/a
31	RAD21	chr12:8230957-8231345	Hela-S3	cervix:	n/a	chr12:8231157-8231176
32	CTCF	chr12:8230194-8231425	A549	lung:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
33	RAD21	chr12:8230661-8231404	SK-N-SH	brain:	n/a	chr12:8231157-8231176
34	CTCF	chr12:8231140-8231290	HCM	heart:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
35	CTCF	chr12:8231120-8231270	GM12874	blood:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
36	CTCF	chr12:8231000-8231300	H1-hESC	embryonic stem cell:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
37	RAD21	chr12:8230900-8231370	H1-hESC	embryonic stem cell:	n/a	chr12:8231157-8231176
38	CTCF	chr12:8231140-8231290	RPTEC	kidney:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
39	CTCF	chr12:8231035-8231302	K562	blood:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
40	SMC3	chr12:8230625-8231403	SK-N-SH	brain:	n/a	chr12:8231161-8231175
41	RAD21	chr12:8231037-8231295	GM12878	blood:	n/a	chr12:8231157-8231176
42	CTCF	chr12:8231120-8231270	HEEpiC	esophagus:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
43	ZNF143	chr12:8230979-8231317	GM12878	blood:	n/a	n/a
44	RAD21	chr12:8231013-8231280	A549	lung:	n/a	chr12:8231157-8231176
45	CTCF	chr12:8230953-8231401	MCF-7	breast:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
46	CTCF	chr12:8230836-8231361	SK-N-SH	brain:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
47	CTCF	chr12:8230978-8231346	IMR90	lung:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
48	CTCF	chr12:8231062-8231293	Spleen_OC	spleen:	n/a	chr12:8231165-8231174 chr12:8231159-8231177
49	RAD21	chr12:8231005-8231296	HepG2	liver:	n/a	chr12:8231157-8231176

No.	Distal block	Cell Line	Cell type
1	chr12:8176284..8181862-chr12:8230041..8234141,6	MCF-7	breast:
2	chr12:8229623..8233032-chr12:8233133..8236264,3	MCF-7	breast:
3	chr12:8226927..8232020-chr12:8232319..8236859,8	K562	blood:
4	chr12:8189586..8192234-chr12:8230888..8234565,4	K562	blood:
5	chr12:8218159..8220408-chr12:8228481..8231320,2	K562	blood:
6	chr12:8198693..8199892-chr12:8230649..8231372,4	K562	blood:
7	chr12:8223318..8224960-chr12:8230452..8232757,2	K562	blood:

Variant related genes	Relation type
NECAP1	TF binding region
ENSG00000171860	Chromatin interaction
ENSG00000089818	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11057087	1.00[AMR][1000 genomes]
rs11567787	1.00[EUR][1000 genomes]
rs11835082	1.00[EUR][1000 genomes]
rs12317265	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12319208	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3759280	1.00[EUR][1000 genomes]
rs7302203	1.00[EUR][1000 genomes]
rs73244571	1.00[EUR][1000 genomes]
rs73244602	1.00[EUR][1000 genomes]
rs73246250	1.00[EUR][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	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	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
8	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
9	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
10	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
11	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
12	nsv1040958	chr12:8177050-8309724	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv541396	chr12:8177050-8309724	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv430460	chr12:8225225-8388656	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:8208600-8233800	Weak transcription	Aorta	Aorta
2	chr12:8219800-8233800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:8223400-8231400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:8223400-8231800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:8229200-8233800	Weak transcription	Liver	Liver
6	chr12:8229600-8231600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:8229800-8231600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:8229800-8231800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:8229800-8233600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:8229800-8233800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:8230000-8233800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:8230000-8233800	Weak transcription	NHLF	lung
13	chr12:8230000-8234000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:8230200-8232400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr12:8230200-8233400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:8230200-8233800	Weak transcription	Osteobl	bone
17	chr12:8230400-8231600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:8230400-8233800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:8230400-8234000	Weak transcription	NH-A	brain
20	chr12:8230600-8231600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:8230600-8232800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:8230600-8233000	Weak transcription	HMEC	breast
23	chr12:8230600-8233000	Weak transcription	NHEK	skin
24	chr12:8230600-8233200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:8230600-8233400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:8230600-8233400	Weak transcription	A549	lung
27	chr12:8230600-8233600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:8230600-8233600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:8230600-8233800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:8230600-8233800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:8230600-8233800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:8230600-8233800	Weak transcription	HSMMtube	muscle
33	chr12:8230600-8234000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:8230800-8231600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:8230800-8232000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr12:8230800-8233200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:8230800-8233400	Weak transcription	HUVEC	blood vessel
38	chr12:8230800-8233600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:8230800-8233800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:8230800-8233800	Weak transcription	HSMM	muscle
41	chr12:8231000-8232200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:8231000-8232200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr12:8231000-8232600	Weak transcription	Hela-S3	cervix
44	chr12:8231000-8233600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:8231000-8233600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:8231000-8233800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:8231000-8233800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:8231000-8233800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:8231000-8233800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:8231000-8233800	Weak transcription	NHDF-Ad	bronchial

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