Variant report

Variant	rs7650554
Chromosome Location	chr3:119758796-119758797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr3:119758117-119758932	K562	blood:	n/a	n/a
2	CBX3	chr3:119758352-119758959	HCT-116	colon:	n/a	n/a
3	KAP1	chr3:119758355-119759353	HEK293	kidney:	n/a	n/a
4	CBX3	chr3:119758473-119758813	K562	blood:	n/a	n/a
5	ZNF143	chr3:119758541-119758825	Hela-S3	cervix:	n/a	n/a
6	TRIM28	chr3:119758540-119758850	K562	blood:	n/a	n/a
7	USF1	chr3:119758432-119758831	HCT-116	colon:	n/a	n/a
8	ZNF143	chr3:119758519-119758828	GM12878	blood:	n/a	n/a
9	CBX3	chr3:119758414-119758873	K562	blood:	n/a	n/a
10	TCF12	chr3:119758330-119758944	A549	lung:	n/a	n/a
11	SETDB1	chr3:119758083-119759298	U2OS	brain:	n/a	n/a
12	ZNF143	chr3:119758525-119758818	K562	blood:	n/a	n/a
13	POLR2A	chr3:119758618-119758820	MCF-7	breast:	n/a	n/a
14	SETDB1	chr3:119758507-119759010	K562	blood:	n/a	n/a
15	BACH1	chr3:119758794-119759273	H1-hESC	embryonic stem cell:	n/a	n/a
16	KAP1	chr3:119758523-119758853	U2OS	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119758303..119760523-chr3:119813063..119815758,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241546	TF binding region
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10049256	0.87[CEU][hapmap]
rs10934512	0.87[CEU][hapmap]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1154597	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11921053	0.94[ASN][1000 genomes]
rs12152218	0.87[CEU][hapmap]
rs13312998	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13314595	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1488764	0.87[CEU][hapmap]
rs1626696	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16830683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830689	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1719887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1719888	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs1719889	1.00[CHB][hapmap]
rs1719895	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732165	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1732169	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs182839	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184576	0.85[EUR][1000 genomes]
rs1907681	0.87[CEU][hapmap]
rs2035671	0.87[CEU][hapmap]
rs2035674	0.87[CEU][hapmap]
rs2130000	0.87[CEU][hapmap]
rs2319541	0.87[CEU][hapmap]
rs2319543	0.87[CEU][hapmap]
rs2461827	0.85[ASN][1000 genomes]
rs2874022	0.85[CEU][hapmap]
rs2874023	0.87[CEU][hapmap]
rs3108749	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334535	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs334536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs334538	0.84[CHD][hapmap]
rs334539	0.87[CEU][hapmap]
rs334545	0.81[ASW][hapmap];0.87[CEU][hapmap]
rs334549	0.87[CEU][hapmap]
rs334551	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs334552	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334554	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs334560	1.00[ASN][1000 genomes]
rs334561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs334565	0.81[YRI][hapmap]
rs334566	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3853592	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4072520	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4438691	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4488869	0.87[CEU][hapmap]
rs4605584	0.85[EUR][1000 genomes]
rs4676822	0.87[CEU][hapmap]
rs4688043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60272712	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6438555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6438558	0.87[CEU][hapmap]
rs6438559	0.87[CEU][hapmap]
rs6438564	0.85[CEU][hapmap]
rs6438567	0.87[CEU][hapmap]
rs66650215	0.91[ASN][1000 genomes]
rs6762640	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6764549	0.86[CEU][hapmap]
rs6769435	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6769988	0.87[CEU][hapmap]
rs6770314	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6771023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6774693	0.94[ASN][1000 genomes]
rs6776122	0.87[CEU][hapmap]
rs6779828	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs6781470	0.87[CEU][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790751	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6794478	0.85[CEU][hapmap]
rs6797689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802301	0.84[ASN][1000 genomes]
rs6805931	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617372	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7620750	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs7624540	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7628426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635604	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7636600	0.94[ASN][1000 genomes]
rs7644268	0.87[CEU][hapmap]
rs7652172	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs7653263	0.85[CEU][hapmap]
rs7653396	0.85[CEU][hapmap]
rs902790	0.87[CEU][hapmap]
rs902791	0.87[CEU][hapmap]
rs902794	0.87[CEU][hapmap]
rs902795	0.87[CEU][hapmap]
rs923380	0.87[CEU][hapmap]
rs923726	0.87[CEU][hapmap]
rs923727	0.87[CEU][hapmap]
rs923728	0.87[CEU][hapmap]
rs9289143	0.87[CEU][hapmap]
rs968824	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9784393	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs979682	0.87[CEU][hapmap]
rs9813834	0.87[CEU][hapmap]
rs9829763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9842302	0.87[CEU][hapmap]
rs9851174	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs9853082	0.87[CEU][hapmap]
rs9858566	0.87[CEU][hapmap]
rs9859778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9879992	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119751800-119766800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:119757000-119760000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
3	chr3:119757000-119760800	ZNF genes & repeats	Primary T cells from cord blood	blood
4	chr3:119757000-119765000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr3:119757200-119758800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
6	chr3:119757200-119760800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:119757200-119761200	ZNF genes & repeats	Primary B cells from cord blood	blood
8	chr3:119757200-119763200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr3:119757200-119765800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:119757400-119760400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr3:119757400-119762400	Weak transcription	Pancreas	Pancrea
12	chr3:119757800-119759200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:119757800-119759600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:119757800-119760000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
15	chr3:119757800-119760400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:119757800-119760800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:119757800-119769800	ZNF genes & repeats	Dnd41	blood
18	chr3:119758000-119758800	ZNF genes & repeats	HSMM	muscle
19	chr3:119758000-119759000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr3:119758000-119759600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr3:119758000-119759800	ZNF genes & repeats	Fetal Lung	lung
22	chr3:119758000-119760000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
23	chr3:119758000-119760000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
24	chr3:119758000-119760000	ZNF genes & repeats	NHDF-Ad	bronchial
25	chr3:119758000-119760200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:119758000-119760200	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:119758000-119760200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr3:119758000-119760200	ZNF genes & repeats	Fetal Intestine Small	intestine
29	chr3:119758000-119760200	ZNF genes & repeats	HMEC	breast
30	chr3:119758000-119760200	ZNF genes & repeats	NHEK	skin
31	chr3:119758000-119761400	ZNF genes & repeats	GM12878-XiMat	blood
32	chr3:119758000-119763400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr3:119758200-119758800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:119758200-119759200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
35	chr3:119758200-119759400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr3:119758200-119760000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:119758200-119760000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:119758200-119760000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:119758200-119760000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
40	chr3:119758200-119760200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:119758200-119760800	ZNF genes & repeats	A549	lung
42	chr3:119758400-119759000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
43	chr3:119758400-119759200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr3:119758400-119759400	ZNF genes & repeats	Brain Hippocampus Middle	brain
45	chr3:119758400-119759400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
46	chr3:119758400-119760000	ZNF genes & repeats	Adipose Nuclei	Adipose
47	chr3:119758400-119760200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:119758400-119760200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:119758400-119760200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:119758400-119760200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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