Variant report

Variant	rs7720858
Chromosome Location	chr5:43419859-43419860
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43414209..43417437-chr5:43419319..43422239,3	K562	blood:
2	chr5:43417971..43419894-chr5:43557023..43559068,2	MCF-7	breast:
3	chr5:43401145..43403362-chr5:43418703..43420917,2	MCF-7	breast:
4	chr5:43418413..43420435-chr5:43484021..43485545,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172239	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10066349	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069318	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1025299	1.00[JPT][hapmap]
rs10461740	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10461741	1.00[JPT][hapmap]
rs10941642	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12656248	0.98[ASN][1000 genomes]
rs12656650	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12657635	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12657724	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12659627	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13154319	1.00[CEU][hapmap]
rs13155622	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs13155888	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13159247	1.00[ASN][1000 genomes]
rs13160431	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13165869	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13167785	1.00[ASN][1000 genomes]
rs13167838	1.00[CEU][hapmap]
rs13167974	1.00[ASN][1000 genomes]
rs13168053	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13169908	1.00[CEU][hapmap]
rs13173517	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13177107	1.00[JPT][hapmap]
rs13180902	1.00[CEU][hapmap]
rs13186439	1.00[CEU][hapmap]
rs13190188	1.00[ASN][1000 genomes]
rs16873315	0.92[AFR][1000 genomes]
rs16873319	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042950	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs34057521	1.00[ASN][1000 genomes]
rs34087297	0.98[ASN][1000 genomes]
rs34181466	1.00[ASN][1000 genomes]
rs34353246	0.93[ASN][1000 genomes]
rs34388270	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34685576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35141306	1.00[ASN][1000 genomes]
rs35929451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733767	1.00[JPT][hapmap]
rs3756417	1.00[JPT][hapmap]
rs3792917	1.00[JPT][hapmap]
rs3806871	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs3822423	1.00[JPT][hapmap]
rs4264950	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];1.00[ASN][1000 genomes]
rs4438885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529199	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4533897	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4554231	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56729517	0.90[AFR][1000 genomes]
rs6862588	1.00[JPT][hapmap]
rs6886399	0.92[ASW][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes]
rs6889653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6890108	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs6892337	1.00[JPT][hapmap]
rs71629168	1.00[ASN][1000 genomes]
rs71629169	0.98[ASN][1000 genomes]
rs7713529	0.98[ASN][1000 genomes]
rs7731345	0.90[AFR][1000 genomes]
rs7736173	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7736174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737947	1.00[JPT][hapmap]
rs9292877	1.00[JPT][hapmap];1.00[MEX][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7720858	SLC16A3	trans	brain	seeQTL
rs7720858	FABP4	trans	brain	seeQTL
rs7720858	NNT	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43402200-43420200	Weak transcription	Gastric	stomach
2	chr5:43412600-43420400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:43412600-43421600	Weak transcription	Pancreas	Pancrea
4	chr5:43417200-43420200	Weak transcription	HepG2	liver
5	chr5:43417200-43421600	Weak transcription	Fetal Intestine Small	intestine
6	chr5:43417200-43421800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:43417200-43421800	Weak transcription	Hela-S3	cervix
8	chr5:43417600-43420200	Weak transcription	K562	blood
9	chr5:43417600-43421600	Weak transcription	Small Intestine	intestine
10	chr5:43419000-43432600	Weak transcription	Colonic Mucosa	Colon
11	chr5:43419200-43421400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:43419400-43421600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:43419800-43420200	Enhancers	Stomach Mucosa	stomach

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