Variant report

Variant	rs1864403
Chromosome Location	chr10:43604950-43604951
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:43594982..43596781-chr10:43603444..43605896,2	MCF-7	breast:
2	chr10:43602925..43605448-chr10:43606836..43609634,2	K562	blood:
3	chr10:43604452..43607562-chr10:43608780..43611078,3	K562	blood:
4	chr10:43577015..43578995-chr10:43604341..43606597,2	MCF-7	breast:
5	chr10:43521915..43522534-chr10:43604245..43605068,2	MCF-7	breast:
6	chr10:43604834..43606698-chr10:43629827..43631473,2	MCF-7	breast:
7	chr10:43517462..43522124-chr10:43604454..43608281,5	MCF-7	breast:
8	chr10:43601071..43602866-chr10:43603676..43605812,2	K562	blood:

No data

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1254965	0.82[MKK][hapmap]
rs1254968	0.82[MKK][hapmap]
rs12767776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1864401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1864402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864408	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1864410	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2115817	0.82[MKK][hapmap]
rs2251674	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435344	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2435356	1.00[ASW][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2435357	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435358	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2435359	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2435362	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435366	0.88[ASN][1000 genomes]
rs2503848	0.82[MKK][hapmap]
rs2505533	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505535	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505536	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2505537	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505557	0.82[MKK][hapmap]
rs2505990	0.82[EUR][1000 genomes]
rs2505991	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2505994	1.00[ASW][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2505998	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2506004	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506005	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506006	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2506008	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2565200	0.82[MKK][hapmap]
rs2565203	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2565204	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742237	0.82[CHB][hapmap]
rs2742243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742244	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28502801	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28576059	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7092603	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs752977	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv522592	chr10:43574936-43615505	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv522566	chr10:43596728-43610671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1864403	ZNF485	cis	cerebellum	SCAN
rs1864403	CSGALNACT2	cis	parietal	SCAN
rs1864403	CSGALNACT2	cis	cerebellum	SCAN
rs1864403	ALOX5	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43601000-43605800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:43601400-43605000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr10:43601400-43605200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:43601400-43605400	Weak transcription	NHDF-Ad	bronchial
5	chr10:43601400-43605600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:43601400-43605600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:43601400-43605600	Weak transcription	Fetal Lung	lung
8	chr10:43601400-43605600	Weak transcription	HSMM	muscle
9	chr10:43601400-43605800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr10:43601400-43605800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:43601400-43605800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr10:43601400-43605800	Weak transcription	GM12878-XiMat	blood
13	chr10:43601400-43605800	Weak transcription	HMEC	breast
14	chr10:43601400-43606000	Weak transcription	Right Atrium	heart
15	chr10:43601400-43613400	Weak transcription	Liver	Liver
16	chr10:43601400-43632800	Weak transcription	Gastric	stomach
17	chr10:43601600-43605000	Weak transcription	Pancreas	Pancrea
18	chr10:43601600-43605400	Weak transcription	Fetal Thymus	thymus
19	chr10:43601600-43605600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr10:43601600-43605600	Weak transcription	Ovary	ovary
21	chr10:43601600-43606000	Weak transcription	Esophagus	oesophagus
22	chr10:43601600-43606000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr10:43601600-43606200	Weak transcription	Right Ventricle	heart
24	chr10:43601600-43606400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:43601600-43609200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr10:43601600-43611200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr10:43601600-43624800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr10:43601800-43605400	Weak transcription	Fetal Intestine Small	intestine
29	chr10:43602000-43605400	Weak transcription	Fetal Intestine Large	intestine
30	chr10:43602000-43606000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr10:43602000-43606000	Weak transcription	Colonic Mucosa	Colon
32	chr10:43602000-43607600	Weak transcription	HUVEC	blood vessel
33	chr10:43602400-43605400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr10:43602400-43605800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:43602400-43606400	Weak transcription	Spleen	Spleen
36	chr10:43602600-43605400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr10:43602600-43605400	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr10:43602800-43605400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr10:43603000-43605800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:43604000-43606800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr10:43604400-43608000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr10:43604600-43607400	Enhancers	Fetal Muscle Leg	muscle
43	chr10:43604800-43605800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:43604800-43606800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:43604800-43606800	Enhancers	NHEK	skin

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