Variant report

Variant	rs2505506
Chromosome Location	chr10:43645854-43645855
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	chr10:43633148..43634894-chr10:43644340..43646524,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1059484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793422	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10793424	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793426	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10793427	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899778	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899779	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899780	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899781	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899782	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899786	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899787	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11238476	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11238479	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11238481	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11238483	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238485	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238490	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11528481	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12220534	0.86[CEU][hapmap];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[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12220560	0.89[EUR][1000 genomes]
rs12268309	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12356643	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12360493	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12416428	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1254958	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1254959	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1254960	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1254962	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1254963	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1254965	1.00[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];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1254967	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1254968	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1270015	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1317214	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800861	0.88[ASN][1000 genomes]
rs1864399	0.83[ASN][1000 genomes]
rs1864400	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1879310	0.93[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1915142	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2003317	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075910	0.88[ASN][1000 genomes]
rs2075912	0.87[ASW][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2115817	1.00[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];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249005	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2257767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293020	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435337	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435338	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435376	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435377	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2435385	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2460551	0.87[JPT][hapmap]
rs2460556	0.82[JPT][hapmap]
rs2503848	1.00[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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2503849	0.97[ASN][1000 genomes]
rs2503853	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2503860	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2503863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2503864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2503881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505511	0.97[ASN][1000 genomes]
rs2505512	0.87[ASN][1000 genomes]
rs2505514	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2505553	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505557	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2565200	1.00[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];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2565201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742233	0.88[ASN][1000 genomes]
rs2742234	0.88[ASN][1000 genomes]
rs2742235	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2742237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742239	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742240	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742241	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3004214	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs4648313	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60845448	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61268333	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61845684	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7073849	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7093409	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7096500	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7098236	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7098237	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs715106	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs741968	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs871763	0.91[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1042310	chr10:43623060-43688505	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2505506	CSGALNACT2	cis	lung	GTEx
rs2505506	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs2505506	XRCC1	trans	parietal	SCAN
rs2505506	CSGALNACT2	cis	Artery Tibial	GTEx
rs2505506	CSGALNACT2	cis	Nerve Tibial	GTEx
rs2505506	CSGALNACT2	cis	Thyroid	GTEx
rs2505506	CSGALNACT2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43634800-43646800	Weak transcription	Left Ventricle	heart
2	chr10:43634800-43652200	Weak transcription	Gastric	stomach
3	chr10:43635400-43655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:43635600-43647000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
6	chr10:43636400-43647000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:43636600-43646800	Weak transcription	NHLF	lung
8	chr10:43636600-43654800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:43636600-43655600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:43637400-43647000	Weak transcription	HSMMtube	muscle
11	chr10:43637400-43655200	Weak transcription	HSMM	muscle
12	chr10:43637600-43651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:43637600-43652200	Weak transcription	Fetal Thymus	thymus
14	chr10:43638200-43646800	Weak transcription	Thymus	Thymus
15	chr10:43638600-43649000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr10:43639400-43647000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr10:43639400-43650600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr10:43639600-43647000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr10:43640600-43646200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr10:43641000-43646400	Weak transcription	Osteobl	bone
21	chr10:43641200-43646800	Weak transcription	Small Intestine	intestine
22	chr10:43641400-43657400	Weak transcription	A549	lung
23	chr10:43641600-43647000	Weak transcription	Stomach Mucosa	stomach
24	chr10:43641800-43646000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr10:43641800-43646800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:43642000-43646000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr10:43642000-43646000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:43642000-43646800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr10:43642200-43646800	Weak transcription	Psoas Muscle	Psoas
30	chr10:43642600-43647600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr10:43643800-43646000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr10:43643800-43646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr10:43643800-43646200	Weak transcription	NHDF-Ad	bronchial
34	chr10:43643800-43647000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:43644400-43646800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr10:43644800-43652200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:43645000-43646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:43645000-43646800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr10:43645000-43650800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:43645200-43647000	Weak transcription	GM12878-XiMat	blood
41	chr10:43645600-43647600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:43645600-43651600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr10:43645600-43656800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr10:43645800-43646000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr10:43645800-43646200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr10:43645800-43647000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:43645800-43647400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr10:43645800-43647600	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr10:43645800-43647600	Enhancers	Primary T cells from cord blood	blood

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