Variant report

Variant	rs11994409
Chromosome Location	chr8:125318265-125318266
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	chr8:125316492..125318934-chr8:125319063..125321541,2	K562	blood:
2	chr8:125307762..125311080-chr8:125313612..125318794,4	K562	blood:

Variant related genes	Relation type
ENSG00000271975	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10089507	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.98[TSI][hapmap]
rs10092974	0.92[CEU][hapmap];0.91[CHB][hapmap]
rs10102946	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10107757	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10111526	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap]
rs10217100	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11786409	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11998018	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13250065	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4076119	0.92[CEU][hapmap]
rs4131904	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351403	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4464954	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4592013	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4870894	0.83[CEU][hapmap];0.83[MKK][hapmap]
rs5010451	0.80[EUR][1000 genomes]
rs6980763	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6986235	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7004196	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7004771	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7829851	0.86[CHD][hapmap]
rs9656954	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[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	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv521356	chr8:125309055-125404763	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11994409	TMPRSS3	trans	lymphoblastoid	seeQTL
rs11994409	RP11-383J24.6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125301400-125329800	Weak transcription	HSMMtube	muscle
2	chr8:125306200-125328000	Weak transcription	A549	lung
3	chr8:125309400-125331000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr8:125311200-125333600	Weak transcription	Right Ventricle	heart
5	chr8:125312000-125320200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr8:125312000-125323800	Weak transcription	Aorta	Aorta
7	chr8:125312000-125330800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr8:125312400-125319400	Weak transcription	Primary T cells from cord blood	blood
9	chr8:125312400-125331000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr8:125312600-125326000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr8:125312600-125328000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr8:125312600-125329800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr8:125312600-125329800	Weak transcription	Thymus	Thymus
14	chr8:125312600-125330000	Weak transcription	Fetal Stomach	stomach
15	chr8:125312600-125333000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:125312600-125346000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr8:125312800-125319200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:125312800-125323600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr8:125312800-125329800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr8:125312800-125329800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr8:125312800-125331600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr8:125312800-125337800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:125313400-125329800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr8:125314000-125320200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr8:125314000-125326200	Weak transcription	Colon Smooth Muscle	Colon
26	chr8:125314000-125330000	Weak transcription	Left Ventricle	heart
27	chr8:125314200-125330000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:125314200-125332000	Weak transcription	Fetal Intestine Small	intestine
29	chr8:125314200-125340200	Weak transcription	Placenta	Placenta
30	chr8:125315800-125333000	Weak transcription	NH-A	brain
31	chr8:125316400-125333800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr8:125316600-125323600	Weak transcription	HSMM	muscle
33	chr8:125316600-125329800	Weak transcription	Ovary	ovary
34	chr8:125316600-125333600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr8:125316800-125319400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr8:125317000-125319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr8:125317000-125333000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:125317400-125319400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr8:125317400-125322600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr8:125317400-125335000	Weak transcription	Fetal Thymus	thymus
41	chr8:125317600-125330400	Weak transcription	Lung	lung
42	chr8:125317800-125319800	Enhancers	Fetal Heart	heart
43	chr8:125317800-125328400	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr8:125318000-125331000	Weak transcription	Fetal Lung	lung
45	chr8:125318200-125331800	Weak transcription	Primary B cells from cord blood	blood
46	chr8:125318200-125333400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr8:125318200-125333400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links