Variant report

Variant	rs4938010
Chromosome Location	chr11:113245566-113245567
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	chr11:113244577..113246835-chr11:113251285..113252833,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10502173	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs1055075	0.87[CHB][hapmap]
rs1055076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10891541	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10891542	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10891545	0.90[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs11214592	0.83[ASN][1000 genomes]
rs1124492	0.81[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12224538	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12225351	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs12285457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12292113	0.84[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12293753	0.83[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1943622	0.84[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs2187346	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs2276070	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs2288159	0.83[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs2298489	0.83[CHB][hapmap]
rs28712705	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781884	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs4590907	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4938007	0.90[EUR][1000 genomes]
rs4938011	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4938014	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs4987094	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs61492892	0.90[ASN][1000 genomes]
rs6589372	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6589373	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7109196	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs7130431	0.86[CHB][hapmap]
rs713233	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs719803	0.83[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7928201	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7928978	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs7931066	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7949242	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs877138	0.81[CHB][hapmap]
rs948176	0.84[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][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	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4938010	TTC12	cis	multi-tissue	Pritchard
rs4938010	TTC12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113203200-113248200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr11:113229200-113246800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:113229400-113246600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr11:113230600-113246400	Weak transcription	Fetal Heart	heart
5	chr11:113231800-113246000	Weak transcription	Fetal Brain Male	brain
6	chr11:113232200-113257400	Weak transcription	Small Intestine	intestine
7	chr11:113236400-113248200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:113236800-113246200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:113236800-113248400	Weak transcription	Placenta	Placenta
10	chr11:113238000-113248200	Weak transcription	Thymus	Thymus
11	chr11:113239400-113247000	Weak transcription	Left Ventricle	heart
12	chr11:113239400-113248000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:113239400-113248200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:113239400-113248800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:113239400-113251600	Weak transcription	Aorta	Aorta
16	chr11:113239600-113246200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr11:113239600-113248200	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:113239800-113247000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:113240000-113248400	Weak transcription	Pancreas	Pancrea
20	chr11:113240200-113245600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:113240200-113248200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr11:113240200-113258400	Weak transcription	Spleen	Spleen
23	chr11:113240600-113246400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr11:113240800-113255800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:113241000-113246000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:113241000-113246600	Weak transcription	Adipose Nuclei	Adipose
27	chr11:113241600-113247600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:113241800-113248200	Weak transcription	Fetal Stomach	stomach
29	chr11:113241800-113257800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:113242000-113253000	Weak transcription	Brain Substantia Nigra	brain
31	chr11:113243200-113247600	Weak transcription	Fetal Thymus	thymus
32	chr11:113243400-113245600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr11:113243800-113246000	Weak transcription	Liver	Liver
34	chr11:113244000-113245800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:113244200-113255800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr11:113244400-113248200	Weak transcription	HSMMtube	muscle
37	chr11:113244400-113256400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:113244600-113247400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr11:113244600-113248200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:113244600-113248200	Weak transcription	NHDF-Ad	bronchial
41	chr11:113244600-113248400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr11:113244600-113254600	Weak transcription	HSMM	muscle
43	chr11:113244800-113247800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:113244800-113247800	Weak transcription	NHEK	skin
45	chr11:113244800-113248000	Weak transcription	NH-A	brain
46	chr11:113244800-113257400	Weak transcription	Lung	lung
47	chr11:113245000-113247400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:113245000-113247800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr11:113245000-113247800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:113245200-113247600	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links