Variant report

Variant	rs4961194
Chromosome Location	chr8:87494974-87494975
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:68)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:68 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:87494900-87495050	K562	blood:	n/a	n/a
2	ZNF143	chr8:87494933-87495065	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr8:87494752-87495166	GM12878	blood:	n/a	n/a
4	ZNF143	chr8:87494857-87495030	K562	blood:	n/a	n/a
5	CTCF	chr8:87494824-87495143	MCF-7	breast:	n/a	n/a
6	CTCF	chr8:87494960-87495110	A549	lung:	n/a	n/a
7	CTCF	chr8:87494840-87494990	HEK293	kidney:	n/a	n/a
8	CTCF	chr8:87494860-87495010	HCT-116	colon:	n/a	n/a
9	CTCF	chr8:87494920-87495070	GM12873	blood:	n/a	n/a
10	CTCF	chr8:87494876-87495068	GM12892	blood:	n/a	n/a
11	CTCF	chr8:87494940-87495090	WERI-Rb-1	eye:	n/a	n/a
12	CTCF	chr8:87494880-87495030	WERI-Rb-1	eye:	n/a	n/a
13	POLR2A	chr8:87494690-87495183	K562	blood:	n/a	n/a
14	POLR2A	chr8:87489172-87495272	HepG2	liver:	n/a	n/a
15	CTCF	chr8:87494900-87495050	MCF-7	breast:	n/a	n/a
16	CTCF	chr8:87494900-87495050	GM12878	blood:	n/a	n/a
17	CTCF	chr8:87494940-87495090	GM12872	blood:	n/a	n/a
18	CTCF	chr8:87494913-87495047	ProgFib	skin:	n/a	n/a
19	RAD21	chr8:87494853-87495056	K562	blood:	n/a	n/a
20	RAD21	chr8:87494800-87495097	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr8:87494920-87495070	GM12875	blood:	n/a	n/a
22	YY1	chr8:87494957-87495079	K562	blood:	n/a	n/a
23	CTCF	chr8:87494932-87494987	Lung_OC	lung:	n/a	n/a
24	CTCF	chr8:87494900-87495050	GM12873	blood:	n/a	n/a
25	POLR2A	chr8:87494954-87495054	A549	lung:	n/a	n/a
26	CTCF	chr8:87494889-87495042	H1-hESC	embryonic stem cell:	n/a	n/a
27	SMC3	chr8:87494861-87495095	GM12878	blood:	n/a	n/a
28	RAD21	chr8:87494873-87495069	GM12878	blood:	n/a	n/a
29	CTCF	chr8:87494900-87495050	HUVEC	blood vessel:	n/a	n/a
30	CTCF	chr8:87494860-87495010	GM12875	blood:	n/a	n/a
31	CTCF	chr8:87494863-87495072	K562	blood:	n/a	n/a
32	CTCF	chr8:87494840-87494990	MCF-7	breast:	n/a	n/a
33	RAD21	chr8:87494861-87495090	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr8:87494847-87495059	A549	lung:	n/a	n/a
35	CTCF	chr8:87494858-87495053	GM12878	blood:	n/a	n/a
36	CTCF	chr8:87494845-87495101	MCF-7	breast:	n/a	n/a
37	CTCF	chr8:87494787-87495155	GM12878	blood:	n/a	n/a
38	CTCF	chr8:87494844-87495105	MCF-7	breast:	n/a	n/a
39	CTCF	chr8:87494900-87495050	Caco-2	colon:	n/a	n/a
40	CTCF	chr8:87494860-87495010	AG04449	skin:	n/a	n/a
41	CTCF	chr8:87494900-87495050	A549	lung:	n/a	n/a
42	CTCF	chr8:87494961-87494989	LNCaP	prostate:	n/a	n/a
43	CTCF	chr8:87494920-87495070	RPTEC	kidney:	n/a	n/a
44	CTCF	chr8:87494880-87495030	Caco-2	colon:	n/a	n/a
45	CTCF	chr8:87494915-87495043	NHEK	skin:	n/a	n/a
46	CTCF	chr8:87494825-87495166	K562	blood:	n/a	n/a
47	CTCF	chr8:87494899-87495052	GM19238	blood:	n/a	n/a
48	POLR2A	chr8:87494573-87495249	MCF-7	breast:	n/a	n/a
49	CTCF	chr8:87494862-87495091	MCF-7	breast:	n/a	n/a
50	CTCF	chr8:87494923-87495018	Fibrobl	skin:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:87488822..87490352-chr8:87494282..87496966,2	MCF-7	breast:
2	chr8:87492324..87497991-chr8:87518822..87522169,6	MCF-7	breast:
3	chr8:87485122..87487844-chr8:87492423..87496426,3	K562	blood:
4	chr8:87485122..87487752-chr8:87491882..87495380,3	K562	blood:
5	chr8:87493659..87498581-chr8:87498622..87502865,4	MCF-7	breast:
6	chr8:87489077..87491109-chr8:87492841..87495174,2	K562	blood:

No data

Variant related genes	Relation type
CPNE3	TF binding region
RMDN1	TF binding region
ENSG00000176623	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10088389	0.88[ASN][1000 genomes]
rs10088739	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10092164	0.87[ASN][1000 genomes]
rs10093238	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10093379	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10095129	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10095498	0.82[JPT][hapmap]
rs10096168	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10096443	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10097450	0.82[JPT][hapmap]
rs10103691	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10481198	0.86[YRI][hapmap]
rs10956800	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956853	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1142528	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11775728	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11781016	0.82[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11787318	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12543856	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12544731	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs12546331	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12546802	0.82[JPT][hapmap]
rs12550142	0.82[JPT][hapmap]
rs12679811	0.82[JPT][hapmap]
rs13042	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs13249753	0.82[JPT][hapmap]
rs13251647	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13267782	0.82[JPT][hapmap]
rs13269259	0.82[JPT][hapmap]
rs13281414	0.82[JPT][hapmap]
rs17608967	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1946939	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1946940	0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2953517	0.82[JPT][hapmap]
rs2976201	0.82[JPT][hapmap]
rs3213911	0.89[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs3883910	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903247	0.82[EUR][1000 genomes]
rs4285463	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4490816	0.81[JPT][hapmap]
rs4587306	0.82[JPT][hapmap]
rs4961188	0.82[JPT][hapmap]
rs4961190	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4961193	0.82[JPT][hapmap]
rs4961195	0.81[JPT][hapmap]
rs4961196	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56102132	0.82[ASN][1000 genomes]
rs56122533	0.83[EUR][1000 genomes]
rs56268009	0.86[EUR][1000 genomes]
rs56321721	0.82[EUR][1000 genomes]
rs56365416	0.88[EUR][1000 genomes]
rs62510798	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62510806	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62510845	0.81[EUR][1000 genomes]
rs6415565	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6471273	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6471280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6471296	0.82[JPT][hapmap]
rs6471309	0.82[JPT][hapmap]
rs6471345	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6471349	0.89[ASN][1000 genomes]
rs6471351	0.89[ASN][1000 genomes]
rs6471352	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6471354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6471360	0.82[JPT][hapmap]
rs6981299	0.87[ASN][1000 genomes]
rs6988601	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6994005	0.92[CEU][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs6996052	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs6999022	0.91[ASN][1000 genomes]
rs7003059	0.82[JPT][hapmap]
rs7006017	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7006629	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7015263	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7015490	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7017706	0.82[JPT][hapmap]
rs7017716	0.82[JPT][hapmap]
rs7017719	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7459811	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7459897	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7460251	0.92[CEU][hapmap];0.93[GIH][hapmap];0.85[EUR][1000 genomes]
rs7460286	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7460439	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7461413	0.82[JPT][hapmap]
rs7461624	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs7463186	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7465350	0.89[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs7465511	0.82[JPT][hapmap]
rs7817738	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7818213	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7820234	0.82[JPT][hapmap]
rs7820697	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7822494	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7823154	0.82[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7832493	0.82[JPT][hapmap]
rs7837569	0.82[JPT][hapmap]
rs7839601	0.82[JPT][hapmap]
rs7846090	0.82[JPT][hapmap]
rs9642913	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9773093	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9942792	0.81[JPT][hapmap]
rs9942823	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv971680	chr8:87494100-87495999	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4961194	CALB1	cis	cerebellum	SCAN
rs4961194	FAM82B	Cis_1M	lymphoblastoid	RTeQTL
rs4961194	CPNE3	cis	cerebellum	SCAN
rs4961194	FAM82B	cis	cerebellum	SCAN
rs4961194	FAM82B	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87441800-87507600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr8:87448800-87502800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr8:87457400-87507400	Weak transcription	Brain Angular Gyrus	brain
4	chr8:87459200-87499600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr8:87471000-87497800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr8:87474000-87517000	Weak transcription	Small Intestine	intestine
7	chr8:87479600-87499400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr8:87481800-87507400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr8:87481800-87507600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr8:87481800-87507600	Weak transcription	Esophagus	oesophagus
11	chr8:87482000-87496400	Weak transcription	Brain Anterior Caudate	brain
12	chr8:87482000-87507600	Weak transcription	Fetal Brain Male	brain
13	chr8:87482000-87508200	Weak transcription	Fetal Heart	heart
14	chr8:87482000-87508400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr8:87482200-87495800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr8:87482200-87496400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr8:87482200-87507600	Weak transcription	Colonic Mucosa	Colon
18	chr8:87482400-87517000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr8:87482800-87496400	Weak transcription	Brain Germinal Matrix	brain
20	chr8:87482800-87503400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr8:87482800-87506600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:87482800-87519600	Weak transcription	HUVEC	blood vessel
23	chr8:87483000-87508400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:87483200-87505400	Weak transcription	Hela-S3	cervix
25	chr8:87485000-87501200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr8:87486400-87496200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr8:87487600-87507400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr8:87488200-87507400	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:87488200-87507600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr8:87488400-87519800	Weak transcription	Psoas Muscle	Psoas
31	chr8:87488800-87505400	Weak transcription	Stomach Mucosa	stomach
32	chr8:87489000-87499600	Strong transcription	HSMM	muscle
33	chr8:87490400-87507400	Weak transcription	HSMMtube	muscle
34	chr8:87490600-87495600	Weak transcription	NHEK	skin
35	chr8:87491200-87496200	Weak transcription	NHDF-Ad	bronchial
36	chr8:87491200-87498000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr8:87491200-87507600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr8:87491400-87495600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr8:87492800-87499600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr8:87493200-87496200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr8:87493200-87499600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr8:87493200-87500200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr8:87493800-87495200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr8:87493800-87495200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr8:87493800-87495200	Strong transcription	GM12878-XiMat	blood
46	chr8:87493800-87497600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr8:87493800-87498200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr8:87493800-87498400	Strong transcription	Fetal Intestine Large	intestine
49	chr8:87493800-87498800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:87493800-87499000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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