Variant report

Variant	rs10861400
Chromosome Location	chr12:105731431-105731432
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	chr12:105628021..105630375-chr12:105728752..105731859,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10507190	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10861371	1.00[CHB][hapmap]
rs10861403	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861407	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10861409	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10861411	0.82[EUR][1000 genomes]
rs10861412	0.82[EUR][1000 genomes]
rs10861413	0.80[EUR][1000 genomes]
rs11112434	1.00[CHB][hapmap]
rs11112469	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112470	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11112478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112482	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112483	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11112484	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112485	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11112486	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112487	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112488	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112492	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs11112493	0.82[EUR][1000 genomes]
rs11112494	0.80[EUR][1000 genomes]
rs11112495	0.80[EUR][1000 genomes]
rs11112496	0.80[EUR][1000 genomes]
rs11112497	0.80[EUR][1000 genomes]
rs11112498	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11112499	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11112502	0.80[EUR][1000 genomes]
rs1196748	1.00[CHB][hapmap]
rs1196749	1.00[CHB][hapmap]
rs1196753	1.00[CHB][hapmap]
rs1196754	1.00[CHB][hapmap]
rs1196756	1.00[CHB][hapmap]
rs1196760	1.00[CHB][hapmap]
rs1196777	1.00[CHB][hapmap]
rs1196793	1.00[CHB][hapmap]
rs1196806	1.00[CHB][hapmap]
rs1196852	1.00[CHB][hapmap]
rs1196861	1.00[CHB][hapmap]
rs1196862	1.00[CHB][hapmap]
rs1196864	1.00[CHB][hapmap]
rs12371845	0.80[EUR][1000 genomes]
rs12822081	1.00[CHB][hapmap]
rs12829692	1.00[CEU][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]
rs12829741	0.80[EUR][1000 genomes]
rs12831150	0.85[EUR][1000 genomes]
rs1432592	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[CHB][hapmap]
rs17036960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17041538	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs2440715	1.00[CHB][hapmap]
rs2888846	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34189496	0.86[EUR][1000 genomes]
rs34346262	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35325227	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35335704	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35519603	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4545651	1.00[CHB][hapmap]
rs6797	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs7131942	0.82[EUR][1000 genomes]
rs7299225	1.00[CHB][hapmap]
rs7302174	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7954485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959385	1.00[CHB][hapmap]
rs7968892	0.80[EUR][1000 genomes]
rs7969370	0.80[EUR][1000 genomes]
rs7969665	0.80[EUR][1000 genomes]
rs7972183	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935240	1.00[CHB][hapmap]
rs935241	1.00[CHB][hapmap]
rs935244	1.00[CHB][hapmap]
rs9645791	0.88[CEU][hapmap];1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861400	C12orf75	cis	Artery Tibial	GTEx
rs10861400	C12orf75	cis	Artery Aorta	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105725200-105734600	Weak transcription	Esophagus	oesophagus
2	chr12:105725600-105747200	Weak transcription	Gastric	stomach
3	chr12:105725800-105734600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:105726000-105734600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:105726000-105734600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:105726200-105734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:105727000-105734600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:105727200-105734400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:105727400-105734400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:105727800-105737200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:105728000-105736000	Weak transcription	HUVEC	blood vessel
12	chr12:105728400-105734600	Weak transcription	HSMMtube	muscle
13	chr12:105728600-105734400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:105728600-105734600	Weak transcription	Fetal Stomach	stomach
15	chr12:105728800-105734400	Weak transcription	HMEC	breast
16	chr12:105729000-105732000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:105729000-105732400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:105729000-105733800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:105729000-105734400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:105729000-105734400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:105729200-105731800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr12:105729400-105731600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:105729400-105734400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:105729600-105731600	Genic enhancers	Dnd41	blood
25	chr12:105729600-105732200	Enhancers	Fetal Thymus	thymus
26	chr12:105729800-105731800	Genic enhancers	A549	lung
27	chr12:105729800-105732600	Enhancers	Placenta	Placenta
28	chr12:105729800-105734400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:105729800-105736200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:105729800-105736800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:105729800-105749400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:105730000-105734600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:105730000-105737400	Weak transcription	NH-A	brain
34	chr12:105730200-105732200	Weak transcription	Aorta	Aorta
35	chr12:105730200-105734200	Weak transcription	Primary T cells from cord blood	blood
36	chr12:105730200-105734400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr12:105730200-105734400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:105730200-105734600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:105730200-105734600	Weak transcription	Thymus	Thymus
40	chr12:105730200-105735200	Weak transcription	Stomach Mucosa	stomach
41	chr12:105730400-105732000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:105730400-105734400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:105730600-105732000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:105730600-105732200	Weak transcription	NHDF-Ad	bronchial
45	chr12:105730600-105755400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:105730800-105733600	Weak transcription	NHEK	skin
47	chr12:105730800-105734400	Weak transcription	HSMM	muscle
48	chr12:105731000-105732000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:105731200-105731600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:105731200-105731600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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