Variant report

Variant	rs2640017
Chromosome Location	chr3:141335121-141335122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141331251..141333372-chr3:141334736..141336860,2	K562	blood:
2	chr3:141204106..141207979-chr3:141333280..141335871,3	K562	blood:
3	chr3:141325633..141327918-chr3:141334802..141336687,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11711375	0.88[JPT][hapmap]
rs11917587	0.88[JPT][hapmap]
rs1493209	0.88[JPT][hapmap]
rs1493210	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851438	0.83[JPT][hapmap]
rs16851441	1.00[JPT][hapmap]
rs16851483	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1863867	0.88[JPT][hapmap]
rs2035935	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2035936	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312193	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2639997	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs295300	0.88[CEU][hapmap];0.84[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs295320	0.88[JPT][hapmap]
rs295321	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295323	0.88[JPT][hapmap]
rs295324	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34558081	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3732869	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806646	0.88[JPT][hapmap]
rs3806648	0.90[ASN][1000 genomes]
rs3821709	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3821710	0.88[JPT][hapmap]
rs3821712	0.88[JPT][hapmap]
rs4683404	0.88[JPT][hapmap]
rs4683610	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs4683612	0.88[ASN][1000 genomes]
rs58025624	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60654199	0.82[ASN][1000 genomes]
rs6767158	0.88[JPT][hapmap]
rs6785874	0.88[JPT][hapmap]
rs6795168	0.88[JPT][hapmap]
rs6800122	0.88[JPT][hapmap]
rs6808837	0.88[JPT][hapmap]
rs73871847	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626871	0.88[JPT][hapmap]
rs7627774	0.93[ASN][1000 genomes]
rs7627807	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.93[ASN][1000 genomes]
rs7643837	0.88[JPT][hapmap]
rs9878347	0.83[JPT][hapmap]
rs9879503	0.83[JPT][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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2640017	SLCO2A1	trans	brain	seeQTL
rs2640017	ZBTB38	cis	multi-tissue	Pritchard
rs2640017	ZBTB38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:141313200-141344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:141320400-141337200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:141321800-141342600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:141324200-141336000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:141325000-141338000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:141326600-141335400	Strong transcription	HUVEC	blood vessel
9	chr3:141326800-141335600	Strong transcription	Primary B cells from cord blood	blood
10	chr3:141328800-141336000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:141330000-141338800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:141330200-141336600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:141330200-141338200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:141330400-141335600	Weak transcription	Hela-S3	cervix
15	chr3:141330400-141336400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:141330400-141336400	Weak transcription	NHEK	skin
17	chr3:141330400-141337000	Weak transcription	Lung	lung
18	chr3:141330400-141337400	Weak transcription	HSMMtube	muscle
19	chr3:141330400-141337800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:141330400-141338000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr3:141330400-141342000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:141330400-141342000	Weak transcription	Pancreas	Pancrea
23	chr3:141330400-141343200	Weak transcription	Brain Angular Gyrus	brain
24	chr3:141330400-141344000	Weak transcription	HMEC	breast
25	chr3:141330400-141344600	Weak transcription	NHLF	lung
26	chr3:141330600-141335200	Weak transcription	Spleen	Spleen
27	chr3:141330600-141336400	Weak transcription	Fetal Intestine Small	intestine
28	chr3:141330600-141336800	Weak transcription	Thymus	Thymus
29	chr3:141330600-141337600	Weak transcription	Brain Germinal Matrix	brain
30	chr3:141330600-141338000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:141330600-141338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:141330600-141339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:141330600-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:141330600-141344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:141330600-141344200	Weak transcription	Ovary	ovary
36	chr3:141330800-141336000	Weak transcription	Fetal Intestine Large	intestine
37	chr3:141330800-141338400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:141330800-141338400	Weak transcription	Left Ventricle	heart
39	chr3:141330800-141344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:141331600-141338800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:141331800-141338600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:141332000-141335200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr3:141332000-141335600	Weak transcription	HepG2	liver
44	chr3:141332000-141337600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:141332000-141344600	Weak transcription	NHDF-Ad	bronchial
46	chr3:141332200-141336800	Weak transcription	Liver	Liver
47	chr3:141332200-141337000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:141332200-141337600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:141332200-141338200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:141332200-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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