Variant report

Variant	rs3744139
Chromosome Location	chr17:17045733-17045734
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17043821..17046160-chr17:17108071..17109890,2	MCF-7	breast:
2	chr17:17045331..17046239-chr17:17216672..17217525,2	K562	blood:
3	chr17:16904876..16905537-chr17:17045251..17045788,2	MCF-7	breast:
4	chr17:17041398..17043468-chr17:17045137..17047861,3	K562	blood:

Variant related genes	Relation type
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1047799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1047805	0.90[ASN][1000 genomes]
rs10852844	0.88[ASN][1000 genomes]
rs10852846	0.96[ASN][1000 genomes]
rs11078368	0.87[ASN][1000 genomes]
rs11078371	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs11078372	0.88[ASN][1000 genomes]
rs11078373	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1110505	0.93[ASN][1000 genomes]
rs11551189	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11651938	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11652678	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11654887	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11657189	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11870035	1.00[ASN][1000 genomes]
rs11870483	0.90[ASN][1000 genomes]
rs12451343	0.85[ASN][1000 genomes]
rs12601422	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs12602583	0.90[ASN][1000 genomes]
rs12602592	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12602839	0.87[ASN][1000 genomes]
rs12603417	0.87[ASN][1000 genomes]
rs1567815	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17794784	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292526	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2292530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2349645	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349648	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28452405	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34001712	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34976658	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35650871	0.86[ASN][1000 genomes]
rs3744125	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744127	0.90[ASN][1000 genomes]
rs3744131	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3744132	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3744134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744136	0.94[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3744137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3744138	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3826305	0.89[ASN][1000 genomes]
rs4073688	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[ASN][1000 genomes]
rs4074612	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs4074819	0.98[ASN][1000 genomes]
rs4283273	0.90[ASN][1000 genomes]
rs4321246	0.98[ASN][1000 genomes]
rs4468683	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4629023	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4985703	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4985704	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4985716	0.83[ASN][1000 genomes]
rs4985721	0.89[ASN][1000 genomes]
rs4985728	0.87[ASN][1000 genomes]
rs4985730	0.90[ASN][1000 genomes]
rs4985737	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4985741	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4985742	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4985743	0.89[ASN][1000 genomes]
rs4985745	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56133536	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57729820	0.83[ASN][1000 genomes]
rs58326998	0.96[ASN][1000 genomes]
rs59394251	0.96[ASN][1000 genomes]
rs60128647	0.87[ASN][1000 genomes]
rs61242604	0.83[ASN][1000 genomes]
rs7211576	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7212275	0.82[ASN][1000 genomes]
rs7214429	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7216677	0.98[ASN][1000 genomes]
rs7218781	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs73979060	0.87[ASN][1000 genomes]
rs73979078	0.87[ASN][1000 genomes]
rs8066111	0.94[ASN][1000 genomes]
rs8066234	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8069259	0.97[ASN][1000 genomes]
rs8071254	0.83[ASN][1000 genomes]
rs8077360	0.98[ASN][1000 genomes]
rs9893676	0.98[ASN][1000 genomes]
rs9895060	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9897510	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9906028	0.86[ASN][1000 genomes]
rs9907109	0.87[ASN][1000 genomes]
rs9910857	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv984510	chr17:17015688-17048858	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv524958	chr17:17029718-17060805	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3744139	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17029800-17088400	Strong transcription	Dnd41	blood
2	chr17:17030000-17048200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr17:17030000-17052200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
5	chr17:17030200-17051600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr17:17030200-17055000	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr17:17030400-17047600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr17:17030400-17047800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr17:17030400-17055800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:17030400-17059800	Strong transcription	Fetal Intestine Small	intestine
11	chr17:17030400-17079200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
13	chr17:17030600-17051000	Strong transcription	Colonic Mucosa	Colon
14	chr17:17031000-17078800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr17:17031200-17057200	Strong transcription	Primary T cells from cord blood	blood
16	chr17:17031200-17067800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr17:17031400-17051800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:17032000-17055000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr17:17032000-17073800	Strong transcription	Fetal Lung	lung
20	chr17:17032200-17048200	Weak transcription	Right Atrium	heart
21	chr17:17032200-17051800	Strong transcription	Pancreas	Pancrea
22	chr17:17032200-17073600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:17032400-17051600	Strong transcription	Gastric	stomach
24	chr17:17033400-17051000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:17034200-17049400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:17034800-17072800	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr17:17036600-17050200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr17:17037200-17074200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:17038200-17051600	Strong transcription	Rectal Smooth Muscle	rectum
30	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
31	chr17:17038800-17048400	Weak transcription	Fetal Heart	heart
32	chr17:17038800-17058400	Weak transcription	Fetal Brain Male	brain
33	chr17:17039000-17048200	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr17:17039400-17051800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:17039800-17047600	Strong transcription	Small Intestine	intestine
36	chr17:17040600-17047400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr17:17041400-17054200	Strong transcription	Hela-S3	cervix
38	chr17:17041800-17045800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr17:17042200-17045800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:17042200-17046000	Weak transcription	Psoas Muscle	Psoas
41	chr17:17042400-17046200	Genic enhancers	HMEC	breast
42	chr17:17042400-17046400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr17:17042400-17046600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:17042600-17045800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr17:17042800-17045800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:17042800-17046000	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr17:17043000-17045800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:17043000-17045800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:17043000-17046000	Genic enhancers	NHEK	skin
50	chr17:17043000-17055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links