Variant report

Variant	rs62335646
Chromosome Location	chr4:129005188-129005189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128982346..128983856-chr4:129003590..129006434,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138709	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1064205	0.87[ASN][1000 genomes]
rs10857128	0.83[ASN][1000 genomes]
rs10857129	0.82[ASN][1000 genomes]
rs11098946	0.84[ASN][1000 genomes]
rs11098950	0.83[ASN][1000 genomes]
rs11737508	0.87[ASN][1000 genomes]
rs12505717	0.83[ASN][1000 genomes]
rs12506549	0.87[ASN][1000 genomes]
rs12507742	0.83[ASN][1000 genomes]
rs12508837	0.83[ASN][1000 genomes]
rs12509092	0.83[ASN][1000 genomes]
rs12641548	0.84[ASN][1000 genomes]
rs12645291	0.83[ASN][1000 genomes]
rs13102049	0.87[ASN][1000 genomes]
rs13139685	0.84[ASN][1000 genomes]
rs16997980	0.84[ASN][1000 genomes]
rs1870686	0.83[ASN][1000 genomes]
rs1961274	0.82[ASN][1000 genomes]
rs1975879	0.82[ASN][1000 genomes]
rs1993722	0.84[ASN][1000 genomes]
rs2061571	0.81[ASN][1000 genomes]
rs2100799	0.82[ASN][1000 genomes]
rs2306054	0.87[ASN][1000 genomes]
rs2306055	0.83[ASN][1000 genomes]
rs2391231	0.81[ASN][1000 genomes]
rs34350456	0.84[ASN][1000 genomes]
rs34800130	0.81[ASN][1000 genomes]
rs34823354	0.83[ASN][1000 genomes]
rs35636574	0.83[ASN][1000 genomes]
rs3733320	0.83[ASN][1000 genomes]
rs4527494	0.83[ASN][1000 genomes]
rs4576015	0.81[ASN][1000 genomes]
rs4833394	0.82[ASN][1000 genomes]
rs4833395	0.87[ASN][1000 genomes]
rs4834226	0.81[ASN][1000 genomes]
rs4834228	0.84[ASN][1000 genomes]
rs4834229	0.84[ASN][1000 genomes]
rs4834230	0.83[ASN][1000 genomes]
rs4834233	0.83[ASN][1000 genomes]
rs4834234	0.81[ASN][1000 genomes]
rs57137613	0.82[ASN][1000 genomes]
rs59944017	0.81[ASN][1000 genomes]
rs62335638	0.82[ASN][1000 genomes]
rs62335645	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6534659	0.81[ASN][1000 genomes]
rs6534660	0.82[ASN][1000 genomes]
rs6534661	0.84[ASN][1000 genomes]
rs6534662	0.87[ASN][1000 genomes]
rs6534663	0.86[ASN][1000 genomes]
rs6534666	0.83[ASN][1000 genomes]
rs6815163	0.81[ASN][1000 genomes]
rs6815890	0.81[ASN][1000 genomes]
rs6820515	0.81[ASN][1000 genomes]
rs6834263	0.81[ASN][1000 genomes]
rs6839370	0.83[ASN][1000 genomes]
rs6842281	0.81[ASN][1000 genomes]
rs6851796	0.83[ASN][1000 genomes]
rs6851896	0.81[ASN][1000 genomes]
rs7661888	0.84[ASN][1000 genomes]
rs7671235	0.81[ASN][1000 genomes]
rs7671641	0.83[ASN][1000 genomes]
rs7684955	0.87[ASN][1000 genomes]
rs7691540	0.81[ASN][1000 genomes]
rs7691566	0.86[ASN][1000 genomes]
rs7692797	0.81[ASN][1000 genomes]
rs7696130	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv532740	chr4:128710011-129035335	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS 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	31 gene(s)	inside rSNPs	diseases
6	esv3416036	chr4:128782694-129133956	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1033701	chr4:128803159-129095018	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	esv1841203	chr4:128817558-129043809	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv1029890	chr4:128828468-129041302	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv1817670	chr4:128850073-129012181	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS 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	28 gene(s)	inside rSNPs	diseases
11	esv1821180	chr4:128850073-129012181	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv1018952	chr4:128850790-129082821	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv595388	chr4:128853913-129084831	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
14	nsv1019555	chr4:128901614-129088903	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	esv1829517	chr4:128982085-129012638	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
17	esv1831536	chr4:128982085-129012638	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
18	nsv595392	chr4:128982085-129012638	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
19	nsv595393	chr4:128982137-129012638	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
20	esv1840969	chr4:128982254-129012181	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
21	esv1792524	chr4:128983925-129133826	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128983800-129027600	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:128983800-129066600	Weak transcription	Esophagus	oesophagus
3	chr4:128983800-129066600	Weak transcription	Small Intestine	intestine
4	chr4:128984200-129018800	Weak transcription	A549	lung
5	chr4:128984200-129024800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:128984200-129029000	Weak transcription	Brain Anterior Caudate	brain
7	chr4:128984200-129035200	Weak transcription	NHLF	lung
8	chr4:128984400-129012600	Weak transcription	Lung	lung
9	chr4:128984400-129013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:128984400-129013800	Weak transcription	NHEK	skin
11	chr4:128984400-129018000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:128984400-129020000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:128986400-129014000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:128986400-129019400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:128987200-129018200	Weak transcription	Psoas Muscle	Psoas
16	chr4:128990400-129007400	Weak transcription	Gastric	stomach
17	chr4:128990800-129013800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:128991000-129031000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:128992800-129029000	Weak transcription	Brain Substantia Nigra	brain
20	chr4:128992800-129038400	Weak transcription	Thymus	Thymus
21	chr4:128993800-129012400	Weak transcription	HSMMtube	muscle
22	chr4:128994200-129066400	Weak transcription	Brain Angular Gyrus	brain
23	chr4:128994400-129009600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:128994400-129025200	Weak transcription	Aorta	Aorta
25	chr4:128994800-129031000	Weak transcription	HMEC	breast
26	chr4:128995600-129035800	Weak transcription	Hela-S3	cervix
27	chr4:128996200-129008400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:128997000-129025000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:128997000-129036800	Weak transcription	Colon Smooth Muscle	Colon
30	chr4:128997000-129054200	Weak transcription	Right Ventricle	heart
31	chr4:128997200-129006600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:128997200-129006800	Weak transcription	NHDF-Ad	bronchial
33	chr4:128997400-129037400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:128997800-129029400	Weak transcription	Spleen	Spleen
35	chr4:128998400-129005600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:128998400-129013800	Weak transcription	Fetal Kidney	kidney
37	chr4:128998400-129020000	Weak transcription	Fetal Brain Male	brain
38	chr4:128998400-129029000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr4:128999000-129032000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:128999400-129013800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:128999400-129020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr4:128999400-129022600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:129000200-129009200	Weak transcription	HUVEC	blood vessel
44	chr4:129000200-129020600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:129000200-129066600	Weak transcription	Colonic Mucosa	Colon
46	chr4:129000400-129017400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:129000800-129005600	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:129001200-129018600	Weak transcription	Pancreas	Pancrea
49	chr4:129001400-129005200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:129001400-129018000	Weak transcription	Ovary	ovary

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