Variant report

Variant	rs3936002
Chromosome Location	chr3:155878603-155878604
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	chr3:155870131..155872683-chr3:155876390..155878620,2	K562	blood:
2	chr3:155874004..155875829-chr3:155876476..155878948,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11718399	0.81[MEX][hapmap]
rs13073556	0.81[MEX][hapmap]
rs1488425	0.81[MEX][hapmap]
rs17170	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1984473	0.85[MEX][hapmap]
rs2173492	1.00[JPT][hapmap]
rs3935399	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4076087	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4234309	0.85[ASN][1000 genomes]
rs4234310	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4234311	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4258915	0.82[ASN][1000 genomes]
rs4359774	0.81[MEX][hapmap]
rs4453801	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4472010	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4488791	1.00[JPT][hapmap]
rs4505650	1.00[JPT][hapmap]
rs4530487	0.88[CEU][hapmap]
rs4533601	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4577423	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs4580504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4611771	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4634068	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4679765	1.00[JPT][hapmap]
rs4680238	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.97[ASN][1000 genomes]
rs4680239	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55858430	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441038	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441039	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441040	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6441042	0.81[MEX][hapmap]
rs6441046	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs6775600	1.00[JPT][hapmap]
rs6784723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7625226	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7625723	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7627867	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9814661	0.81[MEX][hapmap]
rs9818040	1.00[JPT][hapmap]
rs9832745	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9856468	0.81[MEX][hapmap]

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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3936002	B3GALNT1	cis	parietal	SCAN
rs3936002	VEPH1	cis	cerebellum	SCAN
rs3936002	SLC33A1	cis	cerebellum	SCAN
rs3936002	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155870400-155917800	Weak transcription	Aorta	Aorta
2	chr3:155877600-155880000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:155877800-155879000	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:155877800-155879600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:155878000-155878800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:155878000-155879400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:155878200-155878800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:155878200-155879000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:155878200-155879200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:155878200-155879400	Enhancers	Primary T cells from cord blood	blood
11	chr3:155878200-155880000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:155878200-155880000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:155878400-155878800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:155878400-155878800	Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr3:155878400-155878800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:155878400-155878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:155878400-155878800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:155878400-155878800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:155878400-155878800	Enhancers	Brain Anterior Caudate	brain
20	chr3:155878400-155878800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr3:155878400-155878800	Active TSS	Duodenum Mucosa	Duodenum
22	chr3:155878400-155878800	Flanking Active TSS	Fetal Kidney	kidney
23	chr3:155878400-155878800	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr3:155878400-155878800	Flanking Active TSS	NH-A	brain
25	chr3:155878400-155879000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:155878400-155879000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:155878400-155879200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:155878400-155879200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:155878400-155879200	Enhancers	Small Intestine	intestine
30	chr3:155878400-155879200	Enhancers	Hela-S3	cervix
31	chr3:155878400-155879400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:155878400-155879600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr3:155878400-155879600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:155878600-155878800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr3:155878600-155878800	Active TSS	Primary hematopoietic stem cells	blood
36	chr3:155878600-155878800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:155878600-155878800	Enhancers	Adipose Nuclei	Adipose
38	chr3:155878600-155878800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr3:155878600-155878800	Active TSS	GM12878-XiMat	blood
40	chr3:155878600-155879000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr3:155878600-155879000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:155878600-155879200	Active TSS	Colon Smooth Muscle	Colon
43	chr3:155878600-155879200	Enhancers	Fetal Thymus	thymus
44	chr3:155878600-155879400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:155878600-155879400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:155878600-155879400	Enhancers	HUVEC	blood vessel
47	chr3:155878600-155880400	Weak transcription	Rectal Mucosa Donor 29	rectum

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