Variant report

Variant	rs10861227
Chromosome Location	chr12:104891152-104891153
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	chr12:104889078..104893153-chr12:104897198..104902053,5	K562	blood:
2	chr12:104889682..104892508-chr12:104899984..104902053,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10778338	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10778339	0.95[ASN][1000 genomes]
rs10861226	1.00[ASW][hapmap];0.93[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];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];1.00[ASN][1000 genomes]
rs10861228	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861229	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10861230	0.95[ASN][1000 genomes]
rs11112082	0.89[YRI][hapmap]
rs11112084	0.96[ASN][1000 genomes]
rs11614905	0.84[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs12306445	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1619845	1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1704907	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1704909	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1795848	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[ASN][1000 genomes]
rs1795849	1.00[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1795850	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs1795873	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1882492	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1882493	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs1922265	0.93[CEU][hapmap];0.82[TSI][hapmap]
rs2141857	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2141858	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178666	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2374399	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.96[ASN][1000 genomes]
rs3924373	0.96[ASN][1000 genomes]
rs56689310	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv868	chr12:104858964-104895572	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10861227	EPHA8	trans	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:104873200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104875200-104895400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:104875200-104897000	Weak transcription	NHEK	skin
5	chr12:104875400-104904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104879600-104893200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:104880000-104893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:104880000-104897800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:104880600-104897000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:104881600-104898600	Weak transcription	A549	lung
11	chr12:104882600-104893200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr12:104882600-104900600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:104884200-104898000	Weak transcription	Gastric	stomach
14	chr12:104885400-104891200	Genic enhancers	Dnd41	blood
15	chr12:104887200-104891200	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr12:104887200-104903000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:104887600-104899400	Enhancers	Fetal Thymus	thymus
18	chr12:104888000-104897200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:104888000-104900200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:104888200-104891400	Weak transcription	Lung	lung
21	chr12:104888200-104893000	Weak transcription	Placenta	Placenta
22	chr12:104888200-104893400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:104888200-104894600	Weak transcription	Esophagus	oesophagus
24	chr12:104888200-104896600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:104888400-104892000	Weak transcription	NH-A	brain
26	chr12:104888400-104893600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:104888400-104895000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr12:104888800-104897000	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:104888800-104898000	Weak transcription	Aorta	Aorta
30	chr12:104889000-104891200	Enhancers	Fetal Stomach	stomach
31	chr12:104889000-104891400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:104889000-104891600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:104889000-104892000	Weak transcription	HSMM	muscle
34	chr12:104889000-104892200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr12:104889000-104892200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:104889000-104892400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr12:104889000-104892400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr12:104889000-104893000	Weak transcription	Colon Smooth Muscle	Colon
39	chr12:104889000-104894600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:104889000-104895000	Enhancers	Primary T cells from cord blood	blood
41	chr12:104889000-104897400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr12:104889200-104891200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr12:104889200-104891200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr12:104889200-104891400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:104889200-104892200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:104889200-104895000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:104889200-104898200	Weak transcription	HSMMtube	muscle
48	chr12:104889400-104891200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr12:104889800-104891600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:104889800-104899000	Weak transcription	Brain Anterior Caudate	brain

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