Variant report

Variant	rs2280788
Chromosome Location	chr17:34207405-34207406
allele	C/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	RXRA	chr17:34207367-34207714	GM12878	blood:	n/a	chr17:34207371-34207393
2	MEF2A	chr17:34207129-34207658	GM12878	blood:	n/a	chr17:34207427-34207441
3	BATF	chr17:34207351-34207686	GM12878	blood:	n/a	n/a
4	POU2F2	chr17:34206992-34207570	GM12878	blood:	n/a	chr17:34207093-34207107 chr17:34207096-34207106 chr17:34207096-34207106 chr17:34207089-34207111
5	RELA	chr17:34206906-34207759	GM19099	blood:	n/a	n/a
6	POU2F2	chr17:34207002-34207528	GM12891	blood:	n/a	chr17:34207093-34207107 chr17:34207096-34207106 chr17:34207096-34207106 chr17:34207089-34207111
7	EGR1	chr17:34207217-34207607	GM12878	blood:	n/a	n/a
8	WRNIP1	chr17:34206877-34208188	GM12878	blood:	n/a	n/a
9	SP1	chr17:34207200-34207660	GM12878	blood:	n/a	n/a
10	ATF2	chr17:34206848-34207769	GM12878	blood:	n/a	n/a
11	BCLAF1	chr17:34207012-34207745	GM12878	blood:	n/a	n/a
12	POU2F2	chr17:34207026-34207601	GM12891	blood:	n/a	chr17:34207093-34207107 chr17:34207096-34207106 chr17:34207096-34207106 chr17:34207089-34207111
13	POLR2A	chr17:34206794-34207513	GM12891	blood:	n/a	n/a
14	TCF3	chr17:34207170-34207424	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:34207045-34207652	GM18526	blood:	n/a	n/a
16	POLR2A	chr17:34206752-34207735	GM12892	blood:	n/a	n/a
17	MEF2A	chr17:34207101-34207634	GM12878	blood:	n/a	chr17:34207427-34207441
18	TAF1	chr17:34207225-34207421	GM12892	blood:	n/a	n/a
19	MTA3	chr17:34206649-34207913	GM12878	blood:	n/a	n/a
20	BHLHE40	chr17:34207027-34207606	GM12878	blood:	n/a	n/a
21	EP300	chr17:34207197-34207781	GM12878	blood:	n/a	chr17:34207484-34207498 chr17:34207477-34207491
22	POLR2A	chr17:34206692-34207624	HL-60	blood:	n/a	n/a
23	MYC	chr17:34207191-34207463	K562	blood:	n/a	chr17:34207338-34207345 chr17:34207337-34207346
24	RELA	chr17:34206888-34208027	GM12878	blood:	n/a	n/a
25	POLR2A	chr17:34206829-34207614	GM12891	blood:	n/a	n/a
26	RELA	chr17:34206846-34207781	GM10847	blood:	n/a	n/a
27	POLR2A	chr17:34207056-34207500	GM12878	blood:	n/a	n/a
28	BCLAF1	chr17:34207071-34207672	GM12878	blood:	n/a	n/a
29	POLR2A	chr17:34206933-34207616	GM12892	blood:	n/a	n/a
30	YY1	chr17:34207134-34207737	GM12892	blood:	n/a	n/a
31	STAT5A	chr17:34207138-34207604	GM12878	blood:	n/a	chr17:34207470-34207478 chr17:34207319-34207331
32	POLR2A	chr17:34207113-34207657	GM15510	blood:	n/a	n/a
33	RUNX3	chr17:34207028-34207799	GM12878	blood:	n/a	n/a
34	POLR2A	chr17:34207038-34207679	GM18505	blood:	n/a	n/a
35	MAX	chr17:34207106-34207578	K562	blood:	n/a	chr17:34207338-34207345 chr17:34207337-34207346
36	CEBPB	chr17:34206667-34207902	GM12878	blood:	n/a	n/a
37	SRF	chr17:34207233-34207472	GM12878	blood:	n/a	n/a
38	TCF12	chr17:34207265-34207551	GM12878	blood:	n/a	n/a
39	POLR2A	chr17:34206876-34207555	GM12878	blood:	n/a	n/a
40	POLR2A	chr17:34206781-34207629	GM12891	blood:	n/a	n/a
41	CHD2	chr17:34207161-34207686	GM12878	blood:	n/a	n/a
42	MAX	chr17:34206939-34207698	GM12878	blood:	n/a	chr17:34207338-34207345 chr17:34207337-34207346
43	NFIC	chr17:34206674-34208045	GM12878	blood:	n/a	n/a
44	RELA	chr17:34206948-34207769	GM19193	blood:	n/a	n/a
45	POLR2A	chr17:34206747-34207748	GM12892	blood:	n/a	n/a
46	MYC	chr17:34206882-34207672	NB4	blood:	n/a	chr17:34207338-34207345 chr17:34207337-34207346 chr17:34206894-34206903
47	STAT1	chr17:34207258-34207758	GM12878	blood:	n/a	chr17:34207470-34207478 chr17:34207319-34207331
48	ATF2	chr17:34207025-34207889	GM12878	blood:	n/a	n/a
49	POLR2A	chr17:34206773-34207699	GM12891	blood:	n/a	n/a
50	ZNF143	chr17:34207195-34207678	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:13484477..13485216-chr17:34207218..34207779,2	NB4	blood:

Variant related genes	Relation type
CCL5	TF binding region
ENSG00000148925	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10451309	0.83[JPT][hapmap]
rs2072667	0.83[AMR][1000 genomes]
rs2242596	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2242597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280783	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2280786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2293789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2526331	0.89[EUR][1000 genomes]
rs2702958	0.89[EUR][1000 genomes]
rs2735499	0.89[EUR][1000 genomes]
rs28914802	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28914816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28914817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28914819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4251700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4251704	1.00[JPT][hapmap]
rs4251710	1.00[JPT][hapmap]
rs4251739	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55680144	0.89[EUR][1000 genomes]
rs55781042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55792948	0.89[EUR][1000 genomes]
rs55799023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55833673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55846484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55906604	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs55915639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55951822	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56029903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56077005	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56111312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56135703	1.00[AFR][1000 genomes]
rs56170514	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56181735	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56221144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56262662	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56305516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56347933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56382694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61737011	0.83[AMR][1000 genomes]
rs62078115	0.83[AMR][1000 genomes]
rs72483217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2280788	GAS2L2	cis	Heart Left Ventricle	GTEx
rs2280788	GAS2L2	cis	Adipose Subcutaneous	GTEx
rs2280788	GAS2L2	cis	Muscle Skeletal	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34192200-34218000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr17:34192400-34213200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:34202600-34207800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr17:34203800-34207800	Active TSS	Primary T helper naive cells from peripheral blood	blood
5	chr17:34204400-34207600	Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr17:34205000-34207600	Active TSS	Duodenum Mucosa	Duodenum
7	chr17:34205600-34207800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr17:34205800-34207600	Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr17:34205800-34207600	Enhancers	K562	blood
10	chr17:34206200-34207600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:34206800-34207800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:34206800-34208000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr17:34206800-34208000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr17:34206800-34208000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:34206800-34208000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr17:34206800-34208000	Enhancers	Placenta	Placenta
17	chr17:34206800-34208000	Flanking Active TSS	GM12878-XiMat	blood
18	chr17:34207000-34207600	Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr17:34207000-34207600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr17:34207000-34207600	Enhancers	Spleen	Spleen
21	chr17:34207000-34207600	Enhancers	Hela-S3	cervix
22	chr17:34207000-34207800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:34207000-34207800	Enhancers	Fetal Thymus	thymus
24	chr17:34207000-34208000	Enhancers	HUVEC	blood vessel
25	chr17:34207200-34207600	Flanking Active TSS	Primary B cells from peripheral blood	blood
26	chr17:34207200-34207600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:34207200-34207800	Enhancers	Fetal Muscle Leg	muscle
28	chr17:34207400-34207600	Active TSS	Primary T cells fromperipheralblood	blood
29	chr17:34207400-34207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:34207400-34207600	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr17:34207400-34219200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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