Variant report

Variant	rs10890800
Chromosome Location	chr11:107904646-107904647
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	chr11:107903551..107905499-chr11:107906430..107908524,2	K562	blood:
2	chr11:107904163..107905821-chr11:107914372..107915966,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10749914	0.82[CEU][hapmap]
rs10789651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890802	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10890803	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10890804	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890805	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10890806	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10890808	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11212491	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11212505	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11212524	0.82[CEU][hapmap]
rs2271852	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3741051	0.85[EUR][1000 genomes]
rs3858395	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950984	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4503496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4568970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4575229	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754286	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130999	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926222	0.82[CEU][hapmap]
rs7930830	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935911	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947410	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv533794	chr11:107349817-108093259	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1049524	chr11:107540937-107954011	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv521771	chr11:107590335-107904646	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1048938	chr11:107604473-107929950	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv2750980	chr11:107720941-107970986	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1047984	chr11:107794729-107950746	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1040345	chr11:107824764-107924309	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv3372573	chr11:107880365-108022895	Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10890800	ACAT1	cis	cerebellum	SCAN
rs10890800	NPAT	cis	parietal	SCAN
rs10890800	GRIA4	cis	parietal	SCAN
rs10890800	PDCD1LG2	trans	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107881000-107904800	Weak transcription	Placenta	Placenta
2	chr11:107882200-107904800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:107882200-107904800	Weak transcription	Fetal Intestine Large	intestine
4	chr11:107882200-107907800	Weak transcription	Fetal Kidney	kidney
5	chr11:107882200-107908000	Weak transcription	A549	lung
6	chr11:107882200-107917000	Weak transcription	NH-A	brain
7	chr11:107882600-107906200	Weak transcription	Fetal Intestine Small	intestine
8	chr11:107884200-107904800	Weak transcription	HUVEC	blood vessel
9	chr11:107884400-107926200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:107884400-107942000	Weak transcription	Esophagus	oesophagus
11	chr11:107884600-107905000	Weak transcription	Brain Germinal Matrix	brain
12	chr11:107884800-107929200	Weak transcription	NHEK	skin
13	chr11:107885200-107904800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:107885200-107906200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr11:107887200-107904800	Weak transcription	Thymus	Thymus
16	chr11:107888600-107905800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:107890800-107926800	Weak transcription	Hela-S3	cervix
18	chr11:107890800-107975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:107891000-107904800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr11:107891000-107904800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:107891000-107904800	Weak transcription	NHLF	lung
22	chr11:107891000-107965800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:107891200-107905600	Weak transcription	Osteobl	bone
24	chr11:107891200-107908000	Weak transcription	NHDF-Ad	bronchial
25	chr11:107891200-107966200	Weak transcription	Small Intestine	intestine
26	chr11:107891400-107905000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr11:107891400-107914600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:107893800-107904800	Weak transcription	Brain Angular Gyrus	brain
29	chr11:107896400-107904800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:107896400-107927400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:107896600-107904800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:107896600-107907400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:107896600-107917600	Weak transcription	Pancreas	Pancrea
34	chr11:107896600-107922800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:107896600-107926600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:107896600-107962000	Weak transcription	Right Ventricle	heart
37	chr11:107896800-107906200	Weak transcription	Right Atrium	heart
38	chr11:107897000-107907600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:107897200-107904800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:107897200-107904800	Weak transcription	Brain Anterior Caudate	brain
41	chr11:107897400-107904800	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:107897400-107904800	Weak transcription	Fetal Stomach	stomach
43	chr11:107897400-107904800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:107897400-107904800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:107897400-107906000	Weak transcription	Spleen	Spleen
46	chr11:107897400-107907800	Weak transcription	Ovary	ovary
47	chr11:107897600-107904800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr11:107898000-107924600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr11:107898200-107904800	Weak transcription	Aorta	Aorta
50	chr11:107899000-107904800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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