Variant report

Variant	rs9837568
Chromosome Location	chr3:196222369-196222370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:196215210..196217235-chr3:196222277..196224657,2	K562	blood:
2	chr3:196221498..196224147-chr3:196224892..196227326,3	K562	blood:
3	chr3:196217384..196220368-chr3:196221757..196224156,3	K562	blood:
4	chr3:196221948..196224037-chr3:196229901..196232321,3	K562	blood:

Variant related genes	Relation type
ENSG00000163961	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11185543	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718980	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11719920	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12635457	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13084212	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13098146	0.94[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13099664	0.87[ASN][1000 genomes]
rs34196595	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34722299	0.92[EUR][1000 genomes]
rs3796129	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4244200	0.93[ASN][1000 genomes]
rs4393941	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4916431	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4916499	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6775484	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6803161	0.83[EUR][1000 genomes]
rs71630192	0.97[EUR][1000 genomes]
rs7430950	0.82[CHD][hapmap]
rs7611980	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612450	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7643192	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7646174	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7646273	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7647487	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9837291	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9843876	0.93[ASN][1000 genomes]
rs9844068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856006	0.93[ASN][1000 genomes]
rs9864836	0.84[MEX][hapmap]
rs9869437	0.88[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
10	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
rs9837568	TCTEX1D2	cis	parietal	SCAN
rs9837568	RNF168	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196197200-196223800	Strong transcription	Fetal Thymus	thymus
2	chr3:196199400-196227000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:196210800-196226000	Weak transcription	Psoas Muscle	Psoas
4	chr3:196213000-196226800	Weak transcription	Fetal Kidney	kidney
5	chr3:196213400-196225800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:196213800-196226600	Weak transcription	Brain Substantia Nigra	brain
7	chr3:196214200-196223000	Weak transcription	Brain Germinal Matrix	brain
8	chr3:196214200-196225000	Weak transcription	Ovary	ovary
9	chr3:196214200-196225400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:196214200-196225400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:196214200-196226000	Weak transcription	A549	lung
12	chr3:196214400-196222400	Weak transcription	HUVEC	blood vessel
13	chr3:196214400-196222600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:196214400-196222800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:196214400-196223000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:196214400-196223000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:196214400-196225000	Weak transcription	Small Intestine	intestine
18	chr3:196214400-196225800	Weak transcription	HSMMtube	muscle
19	chr3:196214400-196225800	Weak transcription	NHEK	skin
20	chr3:196214400-196226000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:196214400-196226000	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:196214400-196226000	Weak transcription	Esophagus	oesophagus
23	chr3:196214400-196226000	Weak transcription	Gastric	stomach
24	chr3:196214400-196226200	Weak transcription	Right Ventricle	heart
25	chr3:196214400-196226400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:196214400-196226600	Weak transcription	Aorta	Aorta
27	chr3:196214400-196226800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:196214400-196226800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:196214400-196226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:196214400-196226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:196214400-196226800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:196214400-196226800	Weak transcription	Pancreas	Pancrea
33	chr3:196214400-196227000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:196214400-196227000	Weak transcription	Fetal Lung	lung
35	chr3:196214400-196227000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:196214400-196228200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:196214600-196223000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:196214600-196223400	Weak transcription	Fetal Brain Female	brain
39	chr3:196214600-196224600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:196214600-196225400	Weak transcription	HMEC	breast
41	chr3:196214600-196226000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:196214600-196226000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:196214600-196226000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:196214600-196226000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:196214600-196226000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:196214600-196226000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:196214600-196226200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:196214600-196226200	Weak transcription	Fetal Brain Male	brain
49	chr3:196214600-196226400	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:196214600-196226400	Weak transcription	Spleen	Spleen

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