Variant report

Variant	rs11054938
Chromosome Location	chr12:12655145-12655146
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	chr12:12645183..12647034-chr12:12654341..12656540,2	MCF-7	breast:
2	chr12:12652832..12655883-chr12:12662875..12665481,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10845555	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10845558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845564	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845570	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845571	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10845573	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11054927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054931	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11054961	1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12309339	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314295	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12581531	0.89[MEX][hapmap]
rs2417188	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2909054	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2970802	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2970803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4421828	1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4763287	0.96[AMR][1000 genomes]
rs7314806	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7961296	0.86[CHB][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs7978266	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs888201	0.81[CHB][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes]
rs888202	0.96[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
2	chr12:12628800-12655800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr12:12630600-12661200	Weak transcription	NHEK	skin
4	chr12:12630800-12655800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
8	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
9	chr12:12632800-12658200	Weak transcription	Ovary	ovary
10	chr12:12633000-12658600	Weak transcription	Fetal Kidney	kidney
11	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
12	chr12:12634800-12658800	Weak transcription	HSMMtube	muscle
13	chr12:12636200-12655800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:12636800-12656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:12639600-12655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:12639600-12659000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:12640000-12656600	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:12640000-12658000	Weak transcription	NHLF	lung
20	chr12:12640000-12658200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:12640000-12658200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:12640000-12658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr12:12640200-12656600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:12640400-12659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:12641200-12658200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:12641600-12658800	Weak transcription	HUVEC	blood vessel
27	chr12:12641600-12663600	Weak transcription	Lung	lung
28	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:12645400-12655800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr12:12646200-12658200	Weak transcription	Aorta	Aorta
31	chr12:12646400-12655800	Weak transcription	Small Intestine	intestine
32	chr12:12646400-12658000	Weak transcription	K562	blood
33	chr12:12646800-12657400	Weak transcription	Left Ventricle	heart
34	chr12:12646800-12659200	Weak transcription	Gastric	stomach
35	chr12:12647000-12655800	Weak transcription	Psoas Muscle	Psoas
36	chr12:12647000-12661400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:12647800-12655800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:12647800-12658400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:12647800-12659200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:12649200-12658200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:12649200-12658200	Weak transcription	Pancreas	Pancrea
42	chr12:12649400-12658200	Weak transcription	Fetal Lung	lung
43	chr12:12649800-12658200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:12650000-12657200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:12650200-12658000	Weak transcription	Brain Anterior Caudate	brain
46	chr12:12650400-12658600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:12650800-12658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:12652000-12655800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:12652200-12655400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:12652400-12659000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links