Variant report

Variant	rs475043
Chromosome Location	chr11:34493801-34493802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1001179	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs10836230	0.85[CEU][hapmap]
rs10836234	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs11032654	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs11032695	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap]
rs11032718	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11032722	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032723	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032724	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11032726	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11032728	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11604331	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs1267468	1.00[YRI][hapmap]
rs12790145	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12797274	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs12797675	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12804506	0.88[CHD][hapmap];0.86[GIH][hapmap]
rs12804689	0.86[GIH][hapmap]
rs12807961	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs12808450	0.85[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs1408041	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1535719	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17269903	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17269931	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146962	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2231821	0.90[ASN][1000 genomes]
rs2231825	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap]
rs2231828	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420386	0.84[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2476504	1.00[JPT][hapmap]
rs34234992	0.90[ASN][1000 genomes]
rs34366473	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs34901344	0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35495760	0.90[ASN][1000 genomes]
rs4756130	0.82[ASW][hapmap]
rs4756135	1.00[YRI][hapmap]
rs494024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs499406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508370	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs511895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs524167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55898107	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737254	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs475043	CAT	cis	Whole Blood	GTEx
rs475043	CAT	cis	cerebellum	SCAN
rs475043	DEPDC7	cis	parietal	SCAN
rs475043	CAT	cis	lymphoblastoid	seeQTL
rs475043	CAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34470800-34494200	Strong transcription	Brain Germinal Matrix	brain
2	chr11:34470800-34495600	Strong transcription	Stomach Smooth Muscle	stomach
3	chr11:34471000-34494000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr11:34471400-34494000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:34471400-34494600	Strong transcription	Placenta	Placenta
6	chr11:34471400-34495000	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:34471400-34496400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:34471600-34495200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:34471600-34496800	Strong transcription	Duodenum Mucosa	Duodenum
10	chr11:34474000-34496800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:34476200-34495200	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr11:34477200-34495200	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:34482400-34494200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr11:34482400-34495000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr11:34483400-34501600	Weak transcription	HMEC	breast
16	chr11:34487400-34494200	Strong transcription	NH-A	brain
17	chr11:34487800-34494000	Strong transcription	HSMM	muscle
18	chr11:34487800-34494000	Strong transcription	Osteobl	bone
19	chr11:34487800-34494200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:34487800-34494200	Weak transcription	Brain Angular Gyrus	brain
21	chr11:34487800-34495000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:34487800-34496600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:34487800-34496600	Strong transcription	Hela-S3	cervix
24	chr11:34487800-34497000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:34488000-34496400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:34488600-34494000	Strong transcription	NHDF-Ad	bronchial
27	chr11:34488800-34495200	Strong transcription	Ovary	ovary
28	chr11:34489000-34494400	Strong transcription	Fetal Intestine Large	intestine
29	chr11:34489000-34495200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:34489200-34494800	Strong transcription	Primary hematopoietic stem cells	blood
31	chr11:34489200-34495200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:34489200-34495600	Strong transcription	Primary B cells from cord blood	blood
33	chr11:34489400-34494600	Strong transcription	Primary B cells from peripheral blood	blood
34	chr11:34489400-34494800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr11:34489400-34495200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:34489400-34496400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr11:34489400-34496600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:34489400-34496800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:34489600-34494000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:34489600-34494200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr11:34489600-34494400	Strong transcription	Brain Anterior Caudate	brain
42	chr11:34489600-34494600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr11:34489600-34495000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:34489600-34496400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:34489600-34496800	Strong transcription	Adipose Nuclei	Adipose
46	chr11:34489800-34494400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:34489800-34494400	Strong transcription	Aorta	Aorta
48	chr11:34489800-34494400	Strong transcription	Pancreas	Pancrea
49	chr11:34489800-34494400	Strong transcription	Spleen	Spleen
50	chr11:34489800-34494600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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