Variant report

Variant	rs10861406
Chromosome Location	chr12:105754287-105754288
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105753779..105755590-chr12:105767042..105768690,2	MCF-7	breast:
2	chr12:105752392..105754695-chr12:105757650..105760428,2	MCF-7	breast:
3	chr12:105746552..105749035-chr12:105752419..105755099,2	K562	blood:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1061749	0.88[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10735403	0.98[ASN][1000 genomes]
rs10735404	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10746024	0.87[ASN][1000 genomes]
rs10778394	0.88[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10861405	0.83[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap]
rs10861408	0.95[ASN][1000 genomes]
rs10861416	0.91[ASN][1000 genomes]
rs11112491	0.95[ASN][1000 genomes]
rs1432588	0.95[ASN][1000 genomes]
rs2116675	0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6539209	0.81[ASN][1000 genomes]
rs7960794	0.92[ASN][1000 genomes]
rs7962661	0.95[ASN][1000 genomes]
rs8181638	0.96[ASN][1000 genomes]
rs941107	0.83[ASN][1000 genomes]
rs9988966	0.95[ASN][1000 genomes]
rs9989027	0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]

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	nsv899500	chr12:105742674-105803028	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10861406	TXNRD1	cis	parietal	SCAN
rs10861406	BTBD11	cis	cerebellum	SCAN
rs10861406	SYCP3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105730600-105755400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:105734800-105776600	Weak transcription	Esophagus	oesophagus
3	chr12:105735000-105776600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:105735400-105756800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:105735600-105766800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:105735600-105776600	Weak transcription	Fetal Intestine Small	intestine
7	chr12:105746000-105776800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:105747000-105762000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:105747000-105772600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:105747000-105773200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:105747200-105761400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:105747200-105766000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:105747400-105761800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:105747400-105762000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:105748000-105776600	Weak transcription	Gastric	stomach
16	chr12:105748800-105776800	Weak transcription	Pancreas	Pancrea
17	chr12:105749600-105762600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:105749600-105763800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:105749800-105754400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:105749800-105758600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:105749800-105765600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:105750000-105762600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:105751000-105758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:105751000-105769000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:105751200-105755400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:105751200-105759600	Weak transcription	HUVEC	blood vessel
27	chr12:105751200-105766200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:105751200-105776800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:105751400-105755200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:105751400-105756800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:105751400-105762600	Weak transcription	HSMMtube	muscle
32	chr12:105751400-105775200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:105751800-105755000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:105751800-105759000	Weak transcription	HMEC	breast
35	chr12:105752000-105762400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:105752200-105765000	Weak transcription	Stomach Mucosa	stomach
37	chr12:105752400-105758400	Strong transcription	NHDF-Ad	bronchial
38	chr12:105752400-105776400	Weak transcription	Aorta	Aorta
39	chr12:105752600-105755800	Strong transcription	HSMM	muscle
40	chr12:105752600-105757200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:105752600-105757200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:105752600-105769000	Strong transcription	Dnd41	blood
43	chr12:105752800-105755800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:105752800-105759200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:105753200-105759200	Weak transcription	Primary B cells from cord blood	blood
46	chr12:105753600-105755600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr12:105753600-105755800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:105753600-105757200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:105753800-105754400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:105753800-105754400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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