Variant report

Variant	rs7652492
Chromosome Location	chr3:47206914-47206915
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	HCFC1	chr3:47204218-47206975	Hela-S3	cervix:	n/a	n/a
2	CHD1	chr3:47203409-47206971	IMR90	lung:	n/a	chr3:47205244-47205254
3	MXI1	chr3:47203549-47207096	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr3:47205448-47207007	SK-N-SH	brain:	n/a	chr3:47205889-47205902

No.	Distal block	Cell Line	Cell type
1	chr3:47047075..47049174-chr3:47204688..47207568,2	K562	blood:
2	chr3:47206205..47208829-chr3:47228493..47230499,2	K562	blood:
3	chr3:47206330..47207935-chr3:47269635..47272422,2	K562	blood:
4	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:
5	chr3:47206313..47209230-chr3:47234534..47237007,2	K562	blood:
6	chr3:47144386..47146568-chr3:47206115..47208943,2	K562	blood:

Variant related genes	Relation type
SETD2	TF binding region
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 184 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:179)

rs_ID	r²[population]
rs1024036	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1038393	1.00[EUR][1000 genomes]
rs10461017	1.00[EUR][1000 genomes]
rs10461019	1.00[EUR][1000 genomes]
rs10865945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865947	1.00[EUR][1000 genomes]
rs1091068	1.00[EUR][1000 genomes]
rs11130108	1.00[EUR][1000 genomes]
rs11130109	1.00[EUR][1000 genomes]
rs11130122	0.87[AMR][1000 genomes]
rs11706212	1.00[EUR][1000 genomes]
rs11708257	1.00[EUR][1000 genomes]
rs11709693	1.00[EUR][1000 genomes]
rs11709876	1.00[EUR][1000 genomes]
rs11713537	1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs11928558	1.00[EUR][1000 genomes]
rs12330516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12487763	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs13062185	1.00[EUR][1000 genomes]
rs13077134	1.00[EUR][1000 genomes]
rs13078181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13079174	0.87[AMR][1000 genomes]
rs13079416	1.00[EUR][1000 genomes]
rs13082531	1.00[EUR][1000 genomes]
rs13084060	1.00[AMR][1000 genomes]
rs13323092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1378818	1.00[EUR][1000 genomes]
rs1463394	1.00[EUR][1000 genomes]
rs1466272	1.00[EUR][1000 genomes]
rs1466273	1.00[EUR][1000 genomes]
rs1473382	1.00[EUR][1000 genomes]
rs1531874	1.00[EUR][1000 genomes]
rs1563431	1.00[EUR][1000 genomes]
rs1814564	1.00[EUR][1000 genomes]
rs1869870	1.00[EUR][1000 genomes]
rs1872165	1.00[EUR][1000 genomes]
rs1874264	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1979736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2124509	1.00[EUR][1000 genomes]
rs2350642	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2385868	1.00[EUR][1000 genomes]
rs28735306	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295431	1.00[EUR][1000 genomes]
rs295432	1.00[EUR][1000 genomes]
rs295434	1.00[EUR][1000 genomes]
rs295443	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295448	1.00[EUR][1000 genomes]
rs295450	1.00[EUR][1000 genomes]
rs295451	1.00[EUR][1000 genomes]
rs295453	1.00[EUR][1000 genomes]
rs295454	1.00[EUR][1000 genomes]
rs295455	1.00[EUR][1000 genomes]
rs295456	1.00[EUR][1000 genomes]
rs295457	1.00[EUR][1000 genomes]
rs295459	1.00[EUR][1000 genomes]
rs34147581	1.00[EUR][1000 genomes]
rs4018904	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4282092	1.00[EUR][1000 genomes]
rs4289375	1.00[EUR][1000 genomes]
rs4324490	1.00[EUR][1000 genomes]
rs4373094	1.00[EUR][1000 genomes]
rs4378998	1.00[EUR][1000 genomes]
rs4389512	1.00[EUR][1000 genomes]
rs4450857	1.00[EUR][1000 genomes]
rs4478107	1.00[EUR][1000 genomes]
rs448018	1.00[EUR][1000 genomes]
rs4522803	1.00[EUR][1000 genomes]
rs4525902	1.00[EUR][1000 genomes]
rs4543047	1.00[EUR][1000 genomes]
rs4682828	1.00[EUR][1000 genomes]
rs4682832	1.00[EUR][1000 genomes]
rs4682833	1.00[EUR][1000 genomes]
rs4682834	1.00[EUR][1000 genomes]
rs4682835	1.00[EUR][1000 genomes]
rs4682836	1.00[EUR][1000 genomes]
rs4682838	1.00[EUR][1000 genomes]
rs4682841	1.00[EUR][1000 genomes]
rs4682843	1.00[EUR][1000 genomes]
rs4683277	1.00[EUR][1000 genomes]
rs4683279	1.00[EUR][1000 genomes]
rs4683283	1.00[EUR][1000 genomes]
rs4683284	1.00[EUR][1000 genomes]
rs4683285	1.00[EUR][1000 genomes]
rs4683286	1.00[EUR][1000 genomes]
rs4683288	1.00[EUR][1000 genomes]
rs4683289	1.00[EUR][1000 genomes]
rs4683290	1.00[EUR][1000 genomes]
rs4683291	1.00[EUR][1000 genomes]
rs4683292	1.00[EUR][1000 genomes]
rs4683293	1.00[EUR][1000 genomes]
rs4858812	1.00[EUR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442041	1.00[EUR][1000 genomes]
rs6442042	1.00[EUR][1000 genomes]
rs6442043	1.00[EUR][1000 genomes]
rs6442044	1.00[EUR][1000 genomes]
rs6442047	1.00[EUR][1000 genomes]
rs6442048	1.00[EUR][1000 genomes]
rs6442062	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	1.00[EUR][1000 genomes]
rs648226	1.00[EUR][1000 genomes]
rs6766676	1.00[EUR][1000 genomes]
rs6767868	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6768169	1.00[EUR][1000 genomes]
rs6772449	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775797	1.00[EUR][1000 genomes]
rs6778673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6778687	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780994	1.00[EUR][1000 genomes]
rs6785462	1.00[EUR][1000 genomes]
rs6785538	1.00[EUR][1000 genomes]
rs6787210	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6788978	1.00[EUR][1000 genomes]
rs6789730	1.00[EUR][1000 genomes]
rs6804732	1.00[EUR][1000 genomes]
rs6806521	1.00[EUR][1000 genomes]
rs6808117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809904	1.00[EUR][1000 genomes]
rs7372780	1.00[EUR][1000 genomes]
rs73831482	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7615774	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7621530	1.00[EUR][1000 genomes]
rs7624549	1.00[EUR][1000 genomes]
rs7630154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7630904	1.00[EUR][1000 genomes]
rs7638549	1.00[EUR][1000 genomes]
rs7639121	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7643181	1.00[AMR][1000 genomes]
rs7643868	1.00[EUR][1000 genomes]
rs7644043	1.00[EUR][1000 genomes]
rs7644382	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7646076	1.00[EUR][1000 genomes]
rs7649413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649941	1.00[EUR][1000 genomes]
rs7650142	1.00[EUR][1000 genomes]
rs807930	1.00[EUR][1000 genomes]
rs807933	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900688	1.00[EUR][1000 genomes]
rs900689	1.00[EUR][1000 genomes]
rs900690	1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	1.00[EUR][1000 genomes]
rs900694	1.00[EUR][1000 genomes]
rs903538	1.00[AMR][1000 genomes]
rs924009	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs936177	1.00[EUR][1000 genomes]
rs936178	1.00[EUR][1000 genomes]
rs936179	1.00[EUR][1000 genomes]
rs936180	1.00[EUR][1000 genomes]
rs936181	1.00[EUR][1000 genomes]
rs936185	1.00[EUR][1000 genomes]
rs936186	1.00[EUR][1000 genomes]
rs9810881	1.00[EUR][1000 genomes]
rs9812407	1.00[EUR][1000 genomes]
rs9819475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823480	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9826488	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828124	1.00[EUR][1000 genomes]
rs9828473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833500	1.00[EUR][1000 genomes]
rs9852167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861247	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9862711	1.00[EUR][1000 genomes]
rs9869489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878813	1.00[EUR][1000 genomes]
rs9883152	1.00[EUR][1000 genomes]
rs9883909	1.00[EUR][1000 genomes]
rs9990284	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47203000-47207600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:47203200-47207400	Active TSS	GM12878-XiMat	blood
3	chr3:47203200-47207600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:47203400-47207200	Active TSS	Ovary	ovary
5	chr3:47203600-47207200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:47203600-47207200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:47203600-47207200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:47203600-47207200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:47203600-47207200	Active TSS	HSMMtube	muscle
10	chr3:47203800-47207000	Active TSS	Psoas Muscle	Psoas
11	chr3:47203800-47207200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:47203800-47207200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:47203800-47207200	Active TSS	Fetal Intestine Large	intestine
14	chr3:47203800-47207200	Active TSS	Fetal Intestine Small	intestine
15	chr3:47203800-47207200	Active TSS	Stomach Smooth Muscle	stomach
16	chr3:47203800-47207600	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr3:47203800-47207600	Active TSS	H1 Cell Line	embryonic stem cell
18	chr3:47203800-47207600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr3:47204000-47207000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:47204000-47207000	Active TSS	Aorta	Aorta
21	chr3:47204000-47207000	Active TSS	Fetal Stomach	stomach
22	chr3:47204000-47207200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:47204000-47207400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:47204000-47207400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:47204000-47207400	Active TSS	NHDF-Ad	bronchial
26	chr3:47204200-47207000	Active TSS	Colonic Mucosa	Colon
27	chr3:47204200-47207000	Active TSS	Esophagus	oesophagus
28	chr3:47204200-47207000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr3:47204200-47207000	Active TSS	Placenta	Placenta
30	chr3:47204200-47207000	Active TSS	Gastric	stomach
31	chr3:47204200-47207000	Active TSS	Lung	lung
32	chr3:47204200-47207000	Active TSS	Pancreas	Pancrea
33	chr3:47204200-47207000	Active TSS	NH-A	brain
34	chr3:47204200-47207000	Active TSS	NHEK	skin
35	chr3:47204200-47207200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:47204200-47207200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr3:47204200-47207200	Active TSS	Left Ventricle	heart
38	chr3:47204200-47207200	Active TSS	Rectal Smooth Muscle	rectum
39	chr3:47204200-47207400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:47204200-47207400	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr3:47204200-47207400	Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:47204200-47207400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr3:47204200-47207400	Active TSS	A549	lung
44	chr3:47204200-47207400	Active TSS	HSMM	muscle
45	chr3:47204200-47207400	Active TSS	NHLF	lung
46	chr3:47204200-47208000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:47204400-47207000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:47204400-47207000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:47204400-47207000	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr3:47204400-47207000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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