Variant report

Variant	rs1688601
Chromosome Location	chr7:98028160-98028161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97948846..97953573-chr7:98026962..98031463,6	MCF-7	breast:
2	chr7:97948534..97953392-chr7:98027922..98031084,5	MCF-7	breast:
3	chr7:97998858..98000704-chr7:98027178..98028821,2	MCF-7	breast:
4	chr7:97851992..97854043-chr7:98027877..98030619,2	K562	blood:
5	chr7:97987419..97989875-chr7:98026560..98028581,2	K562	blood:

Variant related genes	Relation type
ENSG00000272950	Chromatin interaction
ENSG00000205356	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10228934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10264714	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10280254	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11981805	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12704987	0.94[AMR][1000 genomes]
rs13308560	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs1468339	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes]
rs1635613	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1635614	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs1688604	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];0.97[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];1.00[ASN][1000 genomes]
rs1966359	0.91[AMR][1000 genomes]
rs2452219	0.87[ASN][1000 genomes]
rs3801249	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs73391087	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs757669	0.92[ASW][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers 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	19 gene(s)	inside rSNPs	diseases
7	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv888766	chr7:97975542-98123880	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	esv1795864	chr7:98013507-98040788	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv607919	chr7:98021211-98124854	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97992000-98029400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:97995800-98028200	Weak transcription	Esophagus	oesophagus
3	chr7:98022000-98029200	Weak transcription	Placenta	Placenta
4	chr7:98024200-98028200	Weak transcription	NH-A	brain
5	chr7:98025000-98029000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:98025200-98028400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:98027000-98028200	Active TSS	GM12878-XiMat	blood
8	chr7:98027200-98029000	Weak transcription	Right Atrium	heart
9	chr7:98027600-98028200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr7:98027600-98028200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr7:98027600-98028200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:98027600-98028400	Flanking Active TSS	A549	lung
13	chr7:98027600-98028600	Flanking Active TSS	NHEK	skin
14	chr7:98027600-98029600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:98027600-98030600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:98027800-98028400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr7:98027800-98028400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:98027800-98028400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr7:98027800-98028400	Enhancers	Psoas Muscle	Psoas
20	chr7:98027800-98028400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr7:98027800-98028400	Flanking Active TSS	HMEC	breast
22	chr7:98027800-98028600	Flanking Active TSS	K562	blood
23	chr7:98027800-98029000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:98027800-98030400	Active TSS	Fetal Intestine Small	intestine
25	chr7:98027800-98030400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr7:98027800-98030400	Active TSS	Stomach Mucosa	stomach
27	chr7:98027800-98030800	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr7:98027800-98031000	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr7:98028000-98028200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:98028000-98028200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:98028000-98028200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:98028000-98028200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
33	chr7:98028000-98028200	Active TSS	Fetal Intestine Large	intestine
34	chr7:98028000-98028200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
35	chr7:98028000-98028400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
36	chr7:98028000-98028400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr7:98028000-98028400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:98028000-98028400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr7:98028000-98028400	Active TSS	Gastric	stomach
40	chr7:98028000-98028400	Flanking Active TSS	Pancreas	Pancrea
41	chr7:98028000-98028400	Active TSS	Small Intestine	intestine
42	chr7:98028000-98028600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr7:98028000-98028600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
44	chr7:98028000-98028600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:98028000-98028600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr7:98028000-98028600	Flanking Active TSS	Liver	Liver
47	chr7:98028000-98028600	Enhancers	Fetal Muscle Leg	muscle
48	chr7:98028000-98028600	Enhancers	Left Ventricle	heart
49	chr7:98028000-98028600	Flanking Active TSS	HepG2	liver
50	chr7:98028000-98028600	Enhancers	Osteobl	bone

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