Variant report

Variant	rs2970478
Chromosome Location	chr7:101586146-101586147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101584833..101587634-chr7:101667426..101668972,2	MCF-7	breast:
2	chr7:101524980..101528234-chr7:101584443..101587218,5	MCF-7	breast:
3	chr7:101370298..101373054-chr7:101584171..101586451,2	MCF-7	breast:
4	chr7:101574113..101579725-chr7:101580632..101589310,14	MCF-7	breast:
5	chr7:101455300..101463809-chr7:101582792..101593292,40	MCF-7	breast:
6	chr7:101524538..101530208-chr7:101583819..101590225,13	MCF-7	breast:
7	chr7:101584102..101588182-chr7:101600791..101605094,5	MCF-7	breast:
8	chr7:101552221..101555096-chr7:101584153..101586254,2	MCF-7	breast:
9	chr7:101584411..101586887-chr7:101593987..101597254,4	MCF-7	breast:
10	chr7:101574246..101577081-chr7:101585264..101587735,2	MCF-7	breast:
11	chr7:101585552..101588102-chr7:101621880..101624253,3	MCF-7	breast:
12	chr7:101582848..101590446-chr7:101646237..101653992,20	MCF-7	breast:
13	chr7:101502667..101504998-chr7:101584661..101586646,2	MCF-7	breast:
14	chr7:101574397..101581279-chr7:101584061..101589887,8	K562	blood:
15	chr7:101585477..101587144-chr7:101767345..101769939,2	MCF-7	breast:
16	chr7:101520256..101523208-chr7:101584812..101586417,2	MCF-7	breast:
17	chr7:101582741..101590045-chr7:101612112..101621417,29	MCF-7	breast:
18	chr7:101584190..101586306-chr7:101823871..101825627,2	MCF-7	breast:
19	chr7:101511680..101514939-chr7:101582566..101587455,5	MCF-7	breast:
20	chr7:101457338..101463673-chr7:101582596..101588609,15	MCF-7	breast:
21	chr7:101585316..101588407-chr7:101614430..101618418,4	MCF-7	breast:
22	chr7:101583996..101590317-chr7:101598825..101610404,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272219	Chromatin interaction
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs2906649	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906653	0.88[ASN][1000 genomes]
rs2970477	0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2970493	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2970494	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs385854	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs386137	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs404284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs414438	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs416466	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs425768	0.81[ASN][1000 genomes]
rs425964	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs427039	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs433736	0.85[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs434564	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs439124	0.84[JPT][hapmap]
rs440923	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs441601	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs441780	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4727514	0.83[ASN][1000 genomes]
rs4729764	0.88[CEU][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4729766	0.81[ASN][1000 genomes]
rs6954798	0.82[ASN][1000 genomes]
rs727544	0.86[ASN][1000 genomes]
rs740302	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs876826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv888827	chr7:101562674-101650302	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101567000-101596000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr7:101570200-101597000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:101571600-101587400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:101575800-101587400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:101577600-101595600	Weak transcription	Primary T cells from cord blood	blood
6	chr7:101578200-101612000	Weak transcription	HepG2	liver
7	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:101580400-101587600	Weak transcription	Spleen	Spleen
9	chr7:101580600-101590600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr7:101580600-101590800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr7:101580600-101591200	Weak transcription	Brain Substantia Nigra	brain
12	chr7:101583400-101586200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr7:101583400-101587600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:101583400-101587800	Enhancers	Fetal Thymus	thymus
15	chr7:101583400-101608000	Weak transcription	Primary B cells from cord blood	blood
16	chr7:101583600-101586200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:101583600-101586200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr7:101583600-101586200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr7:101583600-101586400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:101583600-101586400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:101583600-101587400	Enhancers	Fetal Stomach	stomach
22	chr7:101583600-101587800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:101583600-101589400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr7:101583600-101589600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr7:101583600-101591000	Enhancers	Fetal Heart	heart
26	chr7:101583800-101586400	Enhancers	Placenta Amnion	Placenta Amnion
27	chr7:101584000-101586200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:101584000-101586200	Enhancers	Liver	Liver
29	chr7:101584000-101586200	Enhancers	Gastric	stomach
30	chr7:101584000-101586200	Enhancers	Pancreas	Pancrea
31	chr7:101584000-101586200	Enhancers	Thymus	Thymus
32	chr7:101584000-101586400	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr7:101584000-101586400	Enhancers	Colonic Mucosa	Colon
34	chr7:101584000-101586400	Enhancers	Duodenum Mucosa	Duodenum
35	chr7:101584000-101586400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr7:101584000-101586400	Enhancers	K562	blood
37	chr7:101584000-101586600	Enhancers	Fetal Muscle Leg	muscle
38	chr7:101584000-101587000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:101584000-101587000	Genic enhancers	Fetal Intestine Small	intestine
40	chr7:101584000-101587800	Enhancers	Right Atrium	heart
41	chr7:101584000-101589400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr7:101584200-101586200	Flanking Active TSS	A549	lung
43	chr7:101584200-101586200	Enhancers	NH-A	brain
44	chr7:101584200-101586400	Enhancers	HMEC	breast
45	chr7:101584400-101586200	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr7:101584400-101586200	Enhancers	HSMMtube	muscle
47	chr7:101584400-101586400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:101584400-101586400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:101584400-101590600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:101584400-101596200	Weak transcription	Primary B cells from peripheral blood	blood

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