Variant report

Variant	rs2503881
Chromosome Location	chr10:43686026-43686027
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	chr10:43682668..43685704-chr10:43685961..43688550,3	MCF-7	breast:
2	chr10:43684501..43692416-chr10:43693896..43701465,17	K562	blood:

Variant related genes	Relation type
ENSG00000198915	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1059484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793422	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10793424	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10793426	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793427	0.92[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899778	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899779	0.93[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899780	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899781	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899782	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899786	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10899787	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238476	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238479	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238481	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11238483	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11238485	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11238490	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11528481	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220534	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220560	0.90[EUR][1000 genomes]
rs12268309	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12356643	0.96[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12360493	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12416428	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1254958	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1254959	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1254960	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254962	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254963	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254967	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1254968	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1270015	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317214	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800861	0.86[ASN][1000 genomes]
rs1864399	0.81[ASN][1000 genomes]
rs1864400	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1879310	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1915142	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2003317	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075910	0.86[ASN][1000 genomes]
rs2075912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2115817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249005	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2257767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2293020	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435337	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435338	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435339	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435376	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2435377	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435384	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2435385	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2460551	0.87[JPT][hapmap]
rs2460556	0.83[JPT][hapmap]
rs2503848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503849	1.00[ASN][1000 genomes]
rs2503853	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2503860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2503864	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505506	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	0.94[ASN][1000 genomes]
rs2505512	0.84[ASN][1000 genomes]
rs2505514	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2505553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505557	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]
rs2565200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2565201	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742233	0.86[ASN][1000 genomes]
rs2742234	0.86[ASN][1000 genomes]
rs2742235	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2742237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742239	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2742240	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2742241	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3004214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4648313	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60845448	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61268333	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61845684	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7073849	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7093409	0.80[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7096500	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7098236	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7098237	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs715106	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs741968	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs871763	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2503881	CSGALNACT2	cis	Artery Tibial	GTEx
rs2503881	CSGALNACT2	cis	Adipose Subcutaneous	GTEx
rs2503881	CSGALNACT2	cis	Thyroid	GTEx
rs2503881	CSGALNACT2	cis	lung	GTEx
rs2503881	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs2503881	CSGALNACT2	cis	Nerve Tibial	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43635600-43689000	Weak transcription	Esophagus	oesophagus
2	chr10:43652600-43697200	Weak transcription	Pancreas	Pancrea
3	chr10:43658800-43690600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr10:43660400-43687400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:43662200-43697600	Weak transcription	NHEK	skin
6	chr10:43662600-43690000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:43667800-43692800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr10:43668200-43694000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:43669600-43689400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:43671000-43689800	Weak transcription	Gastric	stomach
11	chr10:43672200-43690600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:43673600-43686400	Weak transcription	Colon Smooth Muscle	Colon
13	chr10:43673800-43686400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr10:43674000-43690600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:43674400-43697800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:43675600-43700600	Weak transcription	A549	lung
17	chr10:43675800-43697000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:43676600-43690600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr10:43677200-43692200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr10:43677400-43687400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr10:43678800-43696800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr10:43679400-43687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:43679400-43687400	Weak transcription	Fetal Stomach	stomach
24	chr10:43679400-43687400	Weak transcription	NHLF	lung
25	chr10:43679400-43688000	Weak transcription	Spleen	Spleen
26	chr10:43679400-43688200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr10:43679400-43689800	Weak transcription	Lung	lung
28	chr10:43679400-43690400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:43679400-43692000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr10:43679400-43692200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:43679400-43693400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr10:43679400-43694800	Weak transcription	Brain Substantia Nigra	brain
33	chr10:43679400-43697400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr10:43679600-43686400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr10:43679600-43691800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:43679600-43693200	Weak transcription	Placenta	Placenta
37	chr10:43679800-43687400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr10:43679800-43688000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr10:43679800-43690400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr10:43680000-43691600	Weak transcription	Brain Angular Gyrus	brain
41	chr10:43680000-43697600	Weak transcription	NH-A	brain
42	chr10:43682000-43697400	Weak transcription	Liver	Liver
43	chr10:43682600-43688000	Weak transcription	Thymus	Thymus
44	chr10:43682600-43689200	Weak transcription	Fetal Muscle Leg	muscle
45	chr10:43682600-43690800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr10:43682600-43697400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr10:43682600-43697400	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr10:43682800-43689200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr10:43683000-43687200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:43683000-43687200	Weak transcription	Fetal Brain Female	brain

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