Variant report

Variant	rs2178666
Chromosome Location	chr12:104901914-104901915
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104889078..104893153-chr12:104897198..104902053,5	K562	blood:
2	chr12:104889682..104892508-chr12:104899984..104902053,3	K562	blood:
3	chr12:104900996..104904283-chr12:104904979..104908368,3	K562	blood:

Variant related genes	Relation type
ENSG00000258111	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10778338	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];0.98[ASN][1000 genomes]
rs10778339	0.98[ASN][1000 genomes]
rs10861226	1.00[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]
rs10861227	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]
rs10861228	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];0.98[ASN][1000 genomes]
rs10861229	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10861230	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112084	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11614905	0.84[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12306445	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1619845	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1704907	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1704909	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1795848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795849	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1795850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795873	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1882492	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1882493	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1922265	0.86[CEU][hapmap]
rs2141857	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];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]
rs2141858	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924373	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][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	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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104875400-104904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:104887200-104903000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr12:104890000-104903800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:104893000-104904400	Genic enhancers	Dnd41	blood
5	chr12:104894400-104903800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr12:104894800-104913000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:104895600-104904000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:104897400-104905600	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:104897600-104903600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:104897600-104903800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:104897600-104907800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:104898000-104903200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:104898400-104905000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:104898800-104905200	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr12:104898800-104905600	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr12:104899600-104903600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:104899600-104903800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:104899600-104904000	Weak transcription	A549	lung
19	chr12:104899800-104904000	Weak transcription	HSMMtube	muscle
20	chr12:104899800-104904000	Weak transcription	HUVEC	blood vessel
21	chr12:104900000-104902200	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr12:104900000-104902200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr12:104900000-104903000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr12:104900000-104903600	Weak transcription	Brain Anterior Caudate	brain
25	chr12:104900000-104907200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:104900200-104902000	Enhancers	Right Atrium	heart
27	chr12:104900200-104902200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:104900200-104902800	Enhancers	Fetal Lung	lung
29	chr12:104900200-104904600	Enhancers	Primary T cells fromperipheralblood	blood
30	chr12:104900200-104905400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr12:104900400-104902000	Enhancers	H1 Cell Line	embryonic stem cell
32	chr12:104900400-104902000	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:104900400-104902000	Enhancers	Fetal Brain Male	brain
34	chr12:104900400-104902200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:104900400-104902800	Enhancers	Spleen	Spleen
36	chr12:104900400-104903600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:104900600-104902400	Enhancers	Primary B cells from cord blood	blood
38	chr12:104900600-104904600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:104900800-104903600	Weak transcription	Aorta	Aorta
40	chr12:104900800-104903800	Weak transcription	Small Intestine	intestine
41	chr12:104900800-104904000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:104900800-104904000	Weak transcription	Brain Substantia Nigra	brain
43	chr12:104901000-104902000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:104901000-104903000	ZNF genes & repeats	GM12878-XiMat	blood
45	chr12:104901000-104903800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:104901000-104903800	Weak transcription	Gastric	stomach
47	chr12:104901000-104905600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:104901000-104906400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr12:104901000-104913200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr12:104901200-104902000	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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