Variant report

Variant	rs11185543
Chromosome Location	chr3:196215660-196215661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196215382..196218284-chr3:196226840..196230501,3	K562	blood:
2	chr3:196215210..196217235-chr3:196222277..196224657,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11707744	0.91[ASN][1000 genomes]
rs11718980	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719920	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12632592	0.91[ASN][1000 genomes]
rs12635457	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13084212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098146	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34196595	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34722299	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3796129	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4393941	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4459932	0.80[CEU][hapmap]
rs4916431	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916497	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4916498	0.91[ASN][1000 genomes]
rs4916499	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5016648	0.89[ASN][1000 genomes]
rs55997345	0.89[ASN][1000 genomes]
rs6583305	0.80[CEU][hapmap]
rs6764533	0.80[CEU][hapmap]
rs6772271	0.83[ASN][1000 genomes]
rs6775484	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6803161	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71630192	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433483	0.91[ASN][1000 genomes]
rs7611980	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646174	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646273	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647487	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837568	1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9844068	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9864836	0.96[CHD][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs9869437	0.88[CEU][hapmap];0.98[GIH][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9872866	0.87[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	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv878182	chr3:195974181-196228360	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv469831	chr3:196071603-196235225	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv482542	chr3:196071603-196235225	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	nsv878186	chr3:196158773-196219794	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11185543	RNF168	cis	cerebellum	SCAN
rs11185543	TCTEX1D2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196191800-196216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:196194200-196217400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:196194400-196216600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:196194600-196215800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:196196800-196217000	Strong transcription	Fetal Intestine Small	intestine
6	chr3:196197000-196216800	Strong transcription	GM12878-XiMat	blood
7	chr3:196197000-196220000	Weak transcription	Stomach Mucosa	stomach
8	chr3:196197200-196223800	Strong transcription	Fetal Thymus	thymus
9	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:196200400-196218200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:196210600-196217400	Weak transcription	Fetal Heart	heart
12	chr3:196210600-196219000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:196210800-196226000	Weak transcription	Psoas Muscle	Psoas
14	chr3:196212000-196222000	Weak transcription	HSMM	muscle
15	chr3:196213000-196226800	Weak transcription	Fetal Kidney	kidney
16	chr3:196213200-196222000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:196213400-196225800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:196213800-196226600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:196214200-196217200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:196214200-196223000	Weak transcription	Brain Germinal Matrix	brain
21	chr3:196214200-196225000	Weak transcription	Ovary	ovary
22	chr3:196214200-196225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:196214200-196225400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:196214200-196226000	Weak transcription	A549	lung
25	chr3:196214400-196217200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:196214400-196217400	Weak transcription	Brain Angular Gyrus	brain
27	chr3:196214400-196217600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:196214400-196219800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:196214400-196221400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:196214400-196221600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:196214400-196222000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:196214400-196222000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:196214400-196222400	Weak transcription	HUVEC	blood vessel
34	chr3:196214400-196222600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:196214400-196222800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:196214400-196223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:196214400-196223000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:196214400-196225000	Weak transcription	Small Intestine	intestine
39	chr3:196214400-196225800	Weak transcription	HSMMtube	muscle
40	chr3:196214400-196225800	Weak transcription	NHEK	skin
41	chr3:196214400-196226000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:196214400-196226000	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:196214400-196226000	Weak transcription	Esophagus	oesophagus
44	chr3:196214400-196226000	Weak transcription	Gastric	stomach
45	chr3:196214400-196226200	Weak transcription	Right Ventricle	heart
46	chr3:196214400-196226400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:196214400-196226600	Weak transcription	Aorta	Aorta
48	chr3:196214400-196226800	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr3:196214400-196226800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:196214400-196226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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