Variant report

Variant	rs715106
Chromosome Location	chr10:43616751-43616752
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:43609230..43611797-chr10:43616396..43619297,2	K562	blood:
2	chr10:43616473..43618715-chr10:43626088..43628928,2	MCF-7	breast:
3	chr10:43616569..43618189-chr10:43619172..43621560,2	MCF-7	breast:
4	chr10:43611889..43615361-chr10:43616709..43619694,4	MCF-7	breast:
5	chr10:43616246..43618061-chr10:43622272..43624625,2	K562	blood:
6	chr10:43614895..43617172-chr10:43618877..43621238,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1059484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10793422	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10793424	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10793427	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10899778	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10899779	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10899780	0.80[EUR][1000 genomes]
rs10899781	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10899782	0.82[EUR][1000 genomes]
rs10899786	0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs10899787	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11238476	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11238479	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11238481	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11238483	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11238485	0.80[EUR][1000 genomes]
rs11238490	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs11528481	0.95[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs12220534	0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12220560	0.83[EUR][1000 genomes]
rs12268309	0.84[EUR][1000 genomes]
rs12356643	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12416428	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1254958	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1254959	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1254960	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254962	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254963	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254965	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254967	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1254968	0.86[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1270015	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1317214	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1800861	0.99[ASN][1000 genomes]
rs1864399	0.94[ASN][1000 genomes]
rs1864400	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1879310	0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2003317	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075910	0.99[ASN][1000 genomes]
rs2075912	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2115817	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2249005	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2257767	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293020	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435337	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435338	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435339	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435354	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2435376	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2435377	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435383	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2435385	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2460551	0.87[JPT][hapmap]
rs2460556	0.82[JPT][hapmap]
rs2503848	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503849	0.87[ASN][1000 genomes]
rs2503853	0.95[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap]
rs2503860	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503863	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503864	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2503881	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505506	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2505511	0.92[ASN][1000 genomes]
rs2505512	0.88[ASN][1000 genomes]
rs2505514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2505553	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2505557	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2505994	0.82[MKK][hapmap]
rs2565200	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2565201	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742233	0.99[ASN][1000 genomes]
rs2742234	0.99[ASN][1000 genomes]
rs2742235	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2742237	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742239	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2742241	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3004214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4648313	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60845448	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61268333	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7073849	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7093409	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7096500	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs741968	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871763	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv1038102	chr10:43441601-43642908	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv466880	chr10:43452436-43616751	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
5	nsv550695	chr10:43452436-43616751	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
6	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv1051701	chr10:43555542-43642895	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv1046892	chr10:43609488-43636278	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	esv275022	chr10:43613026-43620551	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs715106	CSGALNACT2	cis	Esophagus Muscularis	GTEx
rs715106	CSGALNACT2	cis	Artery Tibial	GTEx
rs715106	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs715106	CSGALNACT2	cis	lung	GTEx
rs715106	CSGALNACT2	cis	parietal	SCAN
rs715106	CSGALNACT2	cis	Thyroid	GTEx
rs715106	CSGALNACT2	cis	Nerve Tibial	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601400-43632800	Weak transcription	Gastric	stomach
2	chr10:43601600-43624800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr10:43606400-43632600	Weak transcription	Right Atrium	heart
4	chr10:43606600-43616800	Weak transcription	Right Ventricle	heart
5	chr10:43606600-43626000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr10:43606800-43616800	Weak transcription	Fetal Lung	lung
7	chr10:43607800-43617400	Weak transcription	Spleen	Spleen
8	chr10:43609800-43626800	Weak transcription	Fetal Intestine Small	intestine
9	chr10:43611800-43621200	Weak transcription	Fetal Intestine Large	intestine
10	chr10:43614400-43616800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr10:43614400-43617800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr10:43614600-43618400	Weak transcription	Liver	Liver
13	chr10:43614800-43626800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr10:43615000-43618200	Enhancers	Fetal Muscle Trunk	muscle
15	chr10:43615200-43618400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:43615400-43617600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr10:43615400-43617800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr10:43615400-43618600	Enhancers	Primary hematopoietic stem cells	blood
19	chr10:43615400-43619600	Enhancers	Fetal Muscle Leg	muscle
20	chr10:43615600-43617400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr10:43615600-43617800	Enhancers	Placenta	Placenta
22	chr10:43615600-43621400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr10:43615800-43617200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:43615800-43617400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr10:43615800-43617400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr10:43615800-43617400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr10:43615800-43617400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr10:43615800-43617600	Enhancers	Fetal Thymus	thymus
29	chr10:43615800-43617800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr10:43615800-43618000	Enhancers	Primary B cells from peripheral blood	blood
31	chr10:43615800-43618000	Enhancers	GM12878-XiMat	blood
32	chr10:43616000-43617000	Enhancers	Primary T cells from cord blood	blood
33	chr10:43616000-43617200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:43616000-43617200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr10:43616000-43617200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr10:43616000-43617200	Enhancers	Adipose Nuclei	Adipose
37	chr10:43616000-43617400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr10:43616000-43617400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr10:43616000-43617600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:43616000-43617600	Enhancers	Dnd41	blood
41	chr10:43616000-43618000	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr10:43616000-43618000	Enhancers	Primary B cells from cord blood	blood
43	chr10:43616200-43616800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr10:43616200-43617000	Enhancers	Thymus	Thymus
45	chr10:43616200-43617200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr10:43616200-43617400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:43616400-43616800	Enhancers	NH-A	brain
48	chr10:43616400-43617000	Weak transcription	Lung	lung
49	chr10:43616400-43617200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:43616400-43617400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links