Variant report

Variant	rs1562322
Chromosome Location	chr2:85821956-85821957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr2:85821677-85825025	HepG2	liver:	n/a	n/a
2	MTA3	chr2:85821352-85823520	GM12878	blood:	n/a	n/a
3	POLR2A	chr2:85821253-85823228	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:85821727-85823119	GM18505	blood:	n/a	n/a
5	POLR2A	chr2:85821574-85823134	GM12891	blood:	n/a	n/a
6	POLR2A	chr2:85821278-85823600	HUVEC	blood vessel:	n/a	n/a
7	MXI1	chr2:85821708-85824131	IMR90	lung:	n/a	n/a
8	MXI1	chr2:85821768-85823625	SK-N-SH	brain:	n/a	n/a
9	PML	chr2:85821507-85823275	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:85821677-85821999	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:85821587-85824943	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:85821118-85823521	K562	blood:	n/a	n/a
13	NFYB	chr2:85821822-85823090	GM12878	blood:	n/a	chr2:85822706-85822721 chr2:85822787-85822802 chr2:85822785-85822800 chr2:85822706-85822720 chr2:85822708-85822718 chr2:85822785-85822800 chr2:85822787-85822800 chr2:85822786-85822800 chr2:85822788-85822798
14	WRNIP1	chr2:85821575-85822762	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr2:85821853-85823661	MCF-7	breast:	n/a	n/a
16	POLR2A	chr2:85821490-85821982	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:85821637-85823302	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:85821234-85823184	PANC-1	pancreas:	n/a	n/a
19	MYBL2	chr2:85821928-85823514	HepG2	liver:	n/a	n/a
20	POLR2A	chr2:85821369-85825652	HepG2	liver:	n/a	n/a
21	POLR2A	chr2:85821897-85823465	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr2:85821358-85821997	HepG2	liver:	n/a	n/a
23	MXI1	chr2:85821828-85822024	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:85821892-85823289	U87	brain:	n/a	n/a
25	POLR2A	chr2:85821658-85825153	HepG2	liver:	n/a	n/a
26	POLR2A	chr2:85821760-85822090	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:85821843-85823289	U87	brain:	n/a	n/a
28	POLR2A	chr2:85821829-85823306	K562	blood:	n/a	n/a
29	MYBL2	chr2:85821813-85823661	HepG2	liver:	n/a	n/a
30	HCFC1	chr2:85821867-85823682	Hela-S3	cervix:	n/a	n/a
31	PML	chr2:85821696-85823219	K562	blood:	n/a	n/a
32	POLR2A	chr2:85821309-85823251	K562	blood:	n/a	n/a
33	POLR2A	chr2:85821533-85824142	K562	blood:	n/a	n/a
34	RFX5	chr2:85821432-85823573	SK-N-SH	brain:	n/a	chr2:85822709-85822718 chr2:85822788-85822797
35	NFATC1	chr2:85821931-85822938	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:85821479-85823246	H1-hESC	embryonic stem cell:	n/a	n/a
37	STAT5A	chr2:85821569-85823273	GM12878	blood:	n/a	chr2:85822185-85822193
38	POLR2A	chr2:85821954-85823115	GM18526	blood:	n/a	n/a
39	POLR2A	chr2:85821915-85823159	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr2:85821285-85828013	HepG2	liver:	n/a	n/a
41	POLR2A	chr2:85821484-85823489	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:85821319-85823632	HUVEC	blood vessel:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:85821949..85822691-chr3:32022268..32023255,2	Hela-S3	cervix:
2	chr2:85802926..85807956-chr2:85820760..85828546,8	K562	blood:
3	chr1:201984723..201985418-chr2:85821518..85822517,2	Hela-S3	cervix:
4	chr2:85594724..85597082-chr2:85821225..85823571,3	K562	blood:
5	chr2:85647963..85650741-chr2:85821196..85824176,3	K562	blood:
6	chr2:85785429..85790468-chr2:85820934..85826927,9	MCF-7	breast:
7	chr2:85646214..85648407-chr2:85821151..85823018,2	K562	blood:
8	chr2:85764454..85770994-chr2:85819148..85831427,14	K562	blood:
9	chr2:85820402..85822148-chr2:85985989..85987607,2	K562	blood:
10	chr2:85764880..85767543-chr2:85819729..85822384,2	MCF-7	breast:
11	chr2:74683585..74685846-chr2:85821390..85823281,2	MCF-7	breast:
12	chr2:85648213..85650447-chr2:85821641..85823247,2	MCF-7	breast:
13	chr2:85820787..85822313-chr2:86179412..86182366,2	K562	blood:
14	chr2:85765572..85767946-chr2:85820164..85824365,5	MCF-7	breast:
15	chr2:85788313..85790216-chr2:85821578..85824119,2	K562	blood:
16	chr2:85765237..85769549-chr2:85821409..85826975,10	K562	blood:

No data

Variant related genes	Relation type
RNF181	TF binding region
ENSG00000115486	Chromatin interaction
ENSG00000239779	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000242095	Chromatin interaction
ENSG00000152292	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000144645	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10180770	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10182351	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs10190428	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10191726	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10302	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1044158	0.81[CHD][hapmap]
rs1124836	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383605	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]
rs13414982	1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs13418207	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs14242	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1446669	0.90[JPT][hapmap]
rs2028898	0.90[JPT][hapmap]
rs2043675	0.90[JPT][hapmap]
rs2118176	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2232745	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2232747	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2232750	0.90[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304564	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];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2592551	0.90[JPT][hapmap]
rs3024831	1.00[CEU][hapmap];0.90[GIH][hapmap]
rs3198089	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3731828	0.84[JPT][hapmap]
rs3755009	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755010	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821020	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3827550	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6643	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6733550	0.81[CHD][hapmap]
rs6743051	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];0.91[ASN][1000 genomes]
rs699664	0.90[JPT][hapmap]
rs7579147	0.84[JPT][hapmap]
rs7593969	0.84[JPT][hapmap]
rs762684	0.90[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1562322	LOC388969	cis	multi-tissue	Pritchard
rs1562322	VAMP8	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85820000-85822000	Enhancers	Esophagus	oesophagus
2	chr2:85820200-85822000	Enhancers	Right Ventricle	heart
3	chr2:85820600-85822000	Weak transcription	Ovary	ovary
4	chr2:85821200-85822000	Enhancers	Fetal Muscle Trunk	muscle
5	chr2:85821200-85822000	Enhancers	Psoas Muscle	Psoas
6	chr2:85821200-85822000	Enhancers	Right Atrium	heart
7	chr2:85821200-85822200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:85821200-85822200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:85821200-85822200	Enhancers	Spleen	Spleen
10	chr2:85821400-85822000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:85821400-85822000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:85821400-85822000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:85821400-85822000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:85821400-85822000	Enhancers	Fetal Muscle Leg	muscle
15	chr2:85821400-85822000	Enhancers	Placenta	Placenta
16	chr2:85821400-85822000	Enhancers	Fetal Stomach	stomach
17	chr2:85821400-85822000	Enhancers	Gastric	stomach
18	chr2:85821400-85822000	Enhancers	Left Ventricle	heart
19	chr2:85821400-85822000	Flanking Active TSS	GM12878-XiMat	blood
20	chr2:85821400-85822200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:85821400-85822200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:85821400-85822200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:85821400-85822200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr2:85821400-85822200	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr2:85821400-85822200	Flanking Active TSS	Hela-S3	cervix
26	chr2:85821400-85822400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr2:85821400-85822400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr2:85821400-85822400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:85821400-85822400	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr2:85821400-85822400	Flanking Active TSS	Dnd41	blood
31	chr2:85821400-85823400	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:85821400-85823800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr2:85821600-85822000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:85821600-85822000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:85821600-85822000	Enhancers	Colon Smooth Muscle	Colon
36	chr2:85821600-85822000	Enhancers	Small Intestine	intestine
37	chr2:85821600-85822000	Flanking Active TSS	K562	blood
38	chr2:85821600-85822200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:85821600-85822200	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr2:85821600-85822200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr2:85821600-85822200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr2:85821600-85822200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:85821600-85822200	Flanking Active TSS	Brain Angular Gyrus	brain
44	chr2:85821600-85822200	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr2:85821600-85822200	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr2:85821600-85822200	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr2:85821600-85822200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr2:85821600-85822200	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr2:85821600-85822200	Flanking Active TSS	Fetal Lung	lung
50	chr2:85821600-85822200	Flanking Active TSS	Pancreas	Pancrea

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