Variant report

Variant	rs3004214
Chromosome Location	chr10:43631698-43631699
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:43631618-43631714	MCF-7	breast:	n/a	n/a
2	POLR2A	chr10:43631575-43632135	K562	blood:	n/a	n/a
3	POLR2A	chr10:43631040-43635212	IMR90	lung:	n/a	n/a
4	MXI1	chr10:43631456-43635231	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43623070..43625100-chr10:43630988..43633446,2	MCF-7	breast:
2	chr10:43629065..43631893-chr10:43754557..43757372,3	MCF-7	breast:

Variant related genes	Relation type
CSGALNACT2	TF binding region

Extended variants
information (count: 112 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1059484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10793422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10793424	0.83[ASN][1000 genomes]
rs10793426	0.82[ASN][1000 genomes]
rs10793427	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10899778	0.83[ASN][1000 genomes]
rs10899779	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10899780	0.83[ASN][1000 genomes]
rs10899781	0.81[ASN][1000 genomes]
rs10899782	0.83[ASN][1000 genomes]
rs10899786	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10899787	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11238476	0.83[ASN][1000 genomes]
rs11238479	0.83[ASN][1000 genomes]
rs11238481	0.83[ASN][1000 genomes]
rs11238483	0.82[ASN][1000 genomes]
rs11238485	0.81[ASN][1000 genomes]
rs11238490	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11528481	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs12220534	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12268309	0.83[ASN][1000 genomes]
rs12356643	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs12360493	0.83[ASN][1000 genomes]
rs12416428	0.82[ASN][1000 genomes]
rs1254958	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1254959	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1254960	0.91[ASN][1000 genomes]
rs1254962	0.91[ASN][1000 genomes]
rs1254963	0.91[ASN][1000 genomes]
rs1254965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1254967	0.91[ASN][1000 genomes]
rs1254968	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1270015	0.91[ASN][1000 genomes]
rs1272142	0.89[CEU][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1317214	0.81[ASN][1000 genomes]
rs1800861	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1864395	0.89[CEU][hapmap];0.83[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1864399	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1864400	0.94[ASN][1000 genomes]
rs1879310	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1915142	0.81[ASN][1000 genomes]
rs2003317	0.91[ASN][1000 genomes]
rs2075910	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075912	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[ASN][1000 genomes]
rs2075913	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2115817	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2249005	1.00[ASN][1000 genomes]
rs2257767	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2293020	0.91[ASN][1000 genomes]
rs2435337	0.92[ASN][1000 genomes]
rs2435338	0.97[ASN][1000 genomes]
rs2435339	0.97[ASN][1000 genomes]
rs2435354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2435376	0.88[ASN][1000 genomes]
rs2435377	0.91[ASN][1000 genomes]
rs2435383	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2435384	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2435385	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460551	0.87[JPT][hapmap]
rs2460556	0.82[JPT][hapmap]
rs2503841	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2503848	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2503849	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2503853	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2503860	0.91[ASN][1000 genomes]
rs2503863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2503864	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2503865	0.89[CEU][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2503866	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2503881	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2505505	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2505506	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs2505511	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505512	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2505513	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2505514	1.00[ASN][1000 genomes]
rs2505553	0.91[ASN][1000 genomes]
rs2505554	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2505557	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2565200	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2565201	0.97[ASN][1000 genomes]
rs2742233	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742234	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2742235	0.92[ASN][1000 genomes]
rs2742237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742239	0.97[ASN][1000 genomes]
rs2742240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs2742241	1.00[ASN][1000 genomes]
rs3004211	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4648313	0.83[ASN][1000 genomes]
rs60845448	0.83[ASN][1000 genomes]
rs61268333	0.83[ASN][1000 genomes]
rs61845684	0.82[ASN][1000 genomes]
rs7073849	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7093409	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs7096500	0.86[ASN][1000 genomes]
rs7098236	0.83[ASN][1000 genomes]
rs7098237	0.83[ASN][1000 genomes]
rs715106	0.95[ASN][1000 genomes]
rs741968	0.94[ASN][1000 genomes]
rs871763	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
rs3004214	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs3004214	CSGALNACT2	cis	Skin Sun Exposed Lower leg	GTEx
rs3004214	CSGALNACT2	cis	Nerve Tibial	GTEx
rs3004214	CSGALNACT2	cis	Thyroid	GTEx
rs3004214	CSGALNACT2	cis	Esophagus Mucosa	GTEx
rs3004214	CSGALNACT2	cis	Artery Tibial	GTEx
rs3004214	CSGALNACT2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601400-43632800	Weak transcription	Gastric	stomach
2	chr10:43606400-43632600	Weak transcription	Right Atrium	heart
3	chr10:43617200-43632000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:43617400-43632200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:43618000-43632600	Weak transcription	Spleen	Spleen
6	chr10:43622800-43632600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:43623400-43632600	Weak transcription	Primary B cells from cord blood	blood
8	chr10:43624800-43632000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr10:43625200-43632600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr10:43625200-43632600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:43625200-43632600	Weak transcription	Thymus	Thymus
12	chr10:43625600-43632000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr10:43625600-43632000	Weak transcription	Fetal Thymus	thymus
14	chr10:43625600-43632000	Weak transcription	HSMM	muscle
15	chr10:43626000-43632400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:43626400-43631800	Weak transcription	NHDF-Ad	bronchial
17	chr10:43626400-43632600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:43626400-43632600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:43626400-43632800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:43626600-43632000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:43626600-43632000	Weak transcription	Ovary	ovary
22	chr10:43627000-43632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr10:43627000-43632200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr10:43627000-43632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:43627800-43632600	Weak transcription	Fetal Intestine Large	intestine
26	chr10:43628400-43632000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr10:43628800-43632600	Enhancers	GM12878-XiMat	blood
28	chr10:43629200-43631800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:43629200-43632000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr10:43629600-43632000	Weak transcription	Placenta	Placenta
31	chr10:43629600-43633000	Weak transcription	Aorta	Aorta
32	chr10:43629800-43632000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr10:43629800-43632400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:43629800-43632600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr10:43629800-43632600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:43629800-43632600	Weak transcription	Fetal Kidney	kidney
37	chr10:43630200-43632000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:43630400-43632800	Weak transcription	A549	lung
39	chr10:43630600-43632800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr10:43631000-43631800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr10:43631200-43632000	Strong transcription	Osteobl	bone
42	chr10:43631600-43631800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:43631600-43632000	Enhancers	Fetal Brain Male	brain
44	chr10:43631600-43632000	Active TSS	HSMMtube	muscle
45	chr10:43631600-43632200	Enhancers	NHLF	lung
46	chr10:43631600-43632600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr10:43631600-43632600	Enhancers	Fetal Lung	lung
48	chr10:43631600-43632600	Enhancers	Fetal Muscle Leg	muscle

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