Variant report

Variant	rs3756804
Chromosome Location	chr6:46096777-46096778
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr6:46096260-46096788	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:46096074-46098778	GM12891	blood:	n/a	n/a
3	SREBP2	chr6:46096067-46098783	GM12878	blood:	n/a	n/a
4	GATA1	chr6:46096646-46098816	PBDE	blood:	n/a	chr6:46096968-46096978 chr6:46097748-46097756

Variant related genes	Relation type
ENPP4	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12527123	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12529353	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13437614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56139334	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903000	1.00[CEU][hapmap]
rs6926038	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6935013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73735707	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7766857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7772559	0.97[ASN][1000 genomes]
rs9296479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9463179	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9463180	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463181	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463182	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472687	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9472702	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472706	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9472710	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472711	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022912	chr6:46093409-46116449	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3756804	ENPP4	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:46087400-46097000	Weak transcription	Aorta	Aorta
2	chr6:46094200-46096800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:46094400-46096800	Enhancers	Primary B cells from cord blood	blood
4	chr6:46094800-46096800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr6:46095000-46097000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:46095200-46097000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:46095400-46096800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr6:46095400-46097000	Enhancers	Primary B cells from peripheral blood	blood
9	chr6:46095400-46097000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:46095400-46097000	Enhancers	Brain Substantia Nigra	brain
11	chr6:46095400-46097000	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr6:46095600-46096800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:46095600-46096800	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:46095600-46097000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:46095600-46097000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:46095600-46097400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:46095800-46096800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr6:46095800-46097000	Enhancers	Brain Angular Gyrus	brain
19	chr6:46095800-46097000	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:46096000-46096800	Enhancers	Liver	Liver
21	chr6:46096000-46096800	Enhancers	Pancreas	Pancrea
22	chr6:46096000-46096800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr6:46096000-46097000	Enhancers	Brain Hippocampus Middle	brain
24	chr6:46096000-46097200	Flanking Active TSS	Dnd41	blood
25	chr6:46096200-46096800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr6:46096200-46096800	Enhancers	Primary T cells from cord blood	blood
27	chr6:46096200-46096800	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr6:46096200-46097000	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr6:46096200-46097200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr6:46096200-46097400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:46096200-46097600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr6:46096200-46098000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:46096200-46098600	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr6:46096400-46096800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr6:46096400-46096800	Enhancers	Thymus	Thymus
36	chr6:46096400-46097000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr6:46096400-46097000	Enhancers	Fetal Heart	heart
38	chr6:46096400-46097000	Enhancers	Fetal Thymus	thymus
39	chr6:46096400-46098200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:46096400-46098200	Active TSS	Rectal Smooth Muscle	rectum
41	chr6:46096600-46096800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:46096600-46096800	Bivalent Enhancer	Fetal Kidney	kidney
43	chr6:46096600-46096800	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr6:46096600-46097000	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr6:46096600-46097000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr6:46096600-46097000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:46096600-46097000	Active TSS	Adipose Nuclei	Adipose
48	chr6:46096600-46097000	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr6:46096600-46097000	Enhancers	Fetal Intestine Large	intestine
50	chr6:46096600-46097000	Enhancers	Stomach Smooth Muscle	stomach

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