Variant report

Variant	rs13383605
Chromosome Location	chr2:85846329-85846330
allele	A/G
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	POLR2A	chr2:85846261-85846848	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:85845054..85846904-chr2:85859258..85861801,2	MCF-7	breast:
2	chr2:85764765..85769369-chr2:85840508..85847982,10	K562	blood:
3	chr2:85843641..85846530-chr2:85864752..85867588,2	K562	blood:

Variant related genes	Relation type
USP39	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000168883	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10180770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10190428	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10191726	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10302	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1044158	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13414982	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13418207	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14242	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1446669	0.84[JPT][hapmap]
rs1562322	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992151	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2028898	0.84[JPT][hapmap]
rs2043675	0.84[JPT][hapmap]
rs2118176	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232748	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2232750	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304564	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592551	0.84[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3755009	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3755010	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3821020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3827550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6547629	0.81[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6733550	0.80[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6743051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[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]
rs699664	0.84[JPT][hapmap]
rs762684	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13383605	VAMP8	cis	lymphoblastoid	seeQTL
rs13383605	hmm28069	cis	multi-tissue	Pritchard
rs13383605	LOC388969	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85843800-85846800	Weak transcription	Aorta	Aorta
2	chr2:85843800-85876000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:85844200-85848000	Weak transcription	Right Ventricle	heart
4	chr2:85844400-85846400	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr2:85844400-85850800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:85844600-85848200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:85844800-85846400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:85844800-85847800	Weak transcription	Small Intestine	intestine
9	chr2:85844800-85848200	Weak transcription	Gastric	stomach
10	chr2:85844800-85848400	Weak transcription	Colonic Mucosa	Colon
11	chr2:85844800-85858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:85844800-85862600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:85844800-85881600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:85845000-85846400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:85845000-85846400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:85845000-85846400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:85845000-85846400	Weak transcription	Brain Substantia Nigra	brain
18	chr2:85845000-85846400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr2:85845000-85846400	Weak transcription	Fetal Intestine Large	intestine
20	chr2:85845000-85846400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:85845000-85846400	Weak transcription	NHDF-Ad	bronchial
22	chr2:85845000-85846600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:85845000-85846600	Genic enhancers	HepG2	liver
24	chr2:85845000-85846800	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:85845000-85847200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:85845000-85847600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:85845000-85847600	Weak transcription	Fetal Lung	lung
28	chr2:85845000-85847800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:85845000-85847800	Weak transcription	Brain Angular Gyrus	brain
30	chr2:85845000-85848000	Weak transcription	Esophagus	oesophagus
31	chr2:85845000-85848000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:85845000-85848200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:85845000-85848200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:85845000-85848200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:85845000-85848200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:85845000-85848200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:85845000-85848200	Weak transcription	HMEC	breast
38	chr2:85845000-85848200	Weak transcription	HSMMtube	muscle
39	chr2:85845000-85849200	Weak transcription	Pancreas	Pancrea
40	chr2:85845000-85849800	Weak transcription	Fetal Kidney	kidney
41	chr2:85845000-85850000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:85845000-85850600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:85845000-85850800	Weak transcription	Fetal Heart	heart
44	chr2:85845000-85850800	Weak transcription	Stomach Mucosa	stomach
45	chr2:85845000-85852800	Strong transcription	HSMM	muscle
46	chr2:85845000-85876000	Weak transcription	Right Atrium	heart
47	chr2:85845000-85879800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:85845000-85880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr2:85845000-85880800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:85845000-85881400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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