Variant report

Variant	rs12111908
Chromosome Location	chr7:39627782-39627783
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39623431..39626186-chr7:39627006..39629338,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10245247	0.96[ASN][1000 genomes]
rs10258946	1.00[ASN][1000 genomes]
rs10266149	1.00[ASN][1000 genomes]
rs10486798	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10486804	0.92[EUR][1000 genomes]
rs17171603	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17171611	0.92[EUR][1000 genomes]
rs17171613	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17171617	0.92[EUR][1000 genomes]
rs17713754	0.84[ASN][1000 genomes]
rs17713951	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17714049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770594	0.84[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17770625	0.84[ASN][1000 genomes]
rs1989533	0.98[ASN][1000 genomes]
rs2066892	0.92[EUR][1000 genomes]
rs2237500	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2329460	0.87[ASN][1000 genomes]
rs2329461	1.00[ASN][1000 genomes]
rs2329462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2329463	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3213655	1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs3779202	0.92[EUR][1000 genomes]
rs4723881	1.00[ASN][1000 genomes]
rs4723882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4723883	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4723884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4723885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs58299139	0.84[ASN][1000 genomes]
rs59071947	0.84[ASN][1000 genomes]
rs61493712	1.00[ASN][1000 genomes]
rs6968742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs73375695	0.84[ASN][1000 genomes]
rs7785964	0.84[ASN][1000 genomes]
rs7796063	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39607000-39631400	Weak transcription	Aorta	Aorta
2	chr7:39607200-39628800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:39607200-39629000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:39607600-39628600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:39607600-39629400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:39610800-39628800	Weak transcription	GM12878-XiMat	blood
7	chr7:39612400-39628000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:39612600-39628000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:39612600-39629200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:39613400-39628800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:39613800-39628800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:39613800-39629000	Weak transcription	HMEC	breast
13	chr7:39614200-39629200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:39614800-39629200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:39616400-39627800	Weak transcription	Adipose Nuclei	Adipose
16	chr7:39616400-39629000	Weak transcription	Osteobl	bone
17	chr7:39617000-39628200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr7:39617200-39629600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:39617400-39629000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:39618400-39629000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr7:39618400-39633000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:39619000-39628200	Weak transcription	Primary T cells from cord blood	blood
23	chr7:39619000-39629000	Weak transcription	Fetal Thymus	thymus
24	chr7:39619600-39629000	Weak transcription	Fetal Muscle Leg	muscle
25	chr7:39620400-39628600	Weak transcription	NH-A	brain
26	chr7:39620600-39628000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:39620600-39628800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr7:39620800-39627800	Weak transcription	K562	blood
29	chr7:39620800-39628600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:39622600-39629000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:39624000-39629000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:39624000-39629000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr7:39624000-39629200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr7:39624000-39629200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:39624000-39629400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:39624200-39628200	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:39624200-39629000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr7:39626400-39629600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr7:39626400-39635800	Enhancers	HUVEC	blood vessel
40	chr7:39626600-39629200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:39626600-39630200	Enhancers	HSMM	muscle
42	chr7:39627000-39629400	Enhancers	Stomach Mucosa	stomach
43	chr7:39627000-39633200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:39627200-39629200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:39627400-39628800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:39627400-39629000	Weak transcription	NHEK	skin
47	chr7:39627400-39629000	Weak transcription	NHLF	lung
48	chr7:39627600-39630600	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links