Variant report

Variant	rs688020
Chromosome Location	chr7:4228553-4228554
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	chr7:4222010..4223528-chr7:4226659..4228864,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10274810	0.81[ASN][1000 genomes]
rs595784	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs597116	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs604841	0.85[ASN][1000 genomes]
rs60726763	0.84[ASN][1000 genomes]
rs610647	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs625537	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs628060	0.89[JPT][hapmap]
rs635535	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640075	0.89[JPT][hapmap]
rs6462637	0.82[AMR][1000 genomes]
rs649494	0.89[JPT][hapmap]
rs661850	0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs665163	0.89[JPT][hapmap]
rs669153	0.90[ASN][1000 genomes]
rs673500	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs674794	0.86[ASN][1000 genomes]
rs687464	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73674219	0.84[ASN][1000 genomes]
rs7786536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7797803	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs852691	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv464274	chr7:3955516-4613607	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv464275	chr7:3955516-4613607	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv464276	chr7:3955516-4613607	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv464277	chr7:3955516-4613607	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Strong transcription 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 lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv464278	chr7:3955516-4613607	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv605939	chr7:3955516-4613607	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1019305	chr7:3991646-4276004	Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1033687	chr7:4006020-4267871	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv538688	chr7:4006020-4267871	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv917252	chr7:4017819-4374090	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv527624	chr7:4027536-4424054	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv869540	chr7:4063875-4302040	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1016507	chr7:4105420-4255439	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv538691	chr7:4105420-4255439	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	nsv518299	chr7:4116665-4286597	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv538692	chr7:4139994-4265562	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv949581	chr7:4166659-4485938	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv887340	chr7:4167991-4263659	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	esv1820543	chr7:4167991-4286597	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv887341	chr7:4167991-4298625	Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv433015	chr7:4173613-4229445	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv887342	chr7:4182850-4293524	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv1023367	chr7:4192258-4306053	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv887343	chr7:4196046-4263659	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv887344	chr7:4211696-4393478	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:4207800-4228800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:4218000-4230000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr7:4218600-4228800	Weak transcription	Pancreas	Pancrea
4	chr7:4219400-4230000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:4222800-4230200	Weak transcription	Esophagus	oesophagus
6	chr7:4224800-4229000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:4225200-4229800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:4225600-4228800	Weak transcription	Ovary	ovary
9	chr7:4226000-4228800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr7:4226200-4228800	Weak transcription	Fetal Muscle Leg	muscle
11	chr7:4226400-4228800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:4226800-4230200	Weak transcription	Placenta	Placenta
13	chr7:4226800-4235800	Weak transcription	Spleen	Spleen
14	chr7:4227000-4228800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:4227600-4228600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:4227600-4231800	Enhancers	Fetal Brain Male	brain
17	chr7:4227800-4228600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:4227800-4228800	Enhancers	Rectal Smooth Muscle	rectum
19	chr7:4228200-4228800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr7:4228200-4229400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:4228400-4228600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr7:4228400-4228600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:4228400-4228600	Enhancers	Adipose Nuclei	Adipose
24	chr7:4228400-4228600	Enhancers	Brain Hippocampus Middle	brain
25	chr7:4228400-4228600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr7:4228400-4228600	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr7:4228400-4228600	Active TSS	HSMMtube	muscle
28	chr7:4228400-4228800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:4228400-4228800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr7:4228400-4228800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:4228400-4228800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:4228400-4228800	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr7:4228400-4228800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr7:4228400-4229000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:4228400-4229000	Enhancers	Brain Substantia Nigra	brain
36	chr7:4228400-4229000	Enhancers	Fetal Lung	lung
37	chr7:4228400-4229000	Flanking Active TSS	NHEK	skin
38	chr7:4228400-4229200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:4228400-4229200	Enhancers	Brain Cingulate Gyrus	brain
40	chr7:4228400-4229200	Active TSS	Fetal Brain Female	brain
41	chr7:4228400-4229600	Enhancers	Fetal Kidney	kidney
42	chr7:4228400-4230000	Enhancers	Fetal Stomach	stomach
43	chr7:4228400-4230800	Enhancers	Brain Germinal Matrix	brain

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