Variant report

Variant	rs5937
Chromosome Location	chr2:128184770-128184771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:128183770-128186181	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:128184271-128184962	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:128183791-128184931	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:128182379-128188565	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:128183460-128184811	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:128182272-128188076	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:128178778..128180626-chr2:128184042..128185706,2	MCF-7	breast:
2	chr2:128182670..128185856-chr2:128186426..128188335,3	K562	blood:
3	chr2:128172111..128174190-chr2:128184627..128187597,2	MCF-7	breast:
4	chr2:128183243..128185185-chr2:128188049..128189643,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4783	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1011019	1.00[CHB][hapmap]
rs10177052	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1019842	1.00[ASN][1000 genomes]
rs10496661	1.00[ASN][1000 genomes]
rs10803587	1.00[CHB][hapmap]
rs10803589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10850	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1158867	0.86[MEX][hapmap]
rs11679414	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11680877	1.00[ASN][1000 genomes]
rs11683986	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691916	1.00[ASN][1000 genomes]
rs11692990	1.00[ASN][1000 genomes]
rs13030463	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473623	0.81[CEU][hapmap]
rs1504135	1.00[ASN][1000 genomes]
rs1518760	1.00[ASN][1000 genomes]
rs1568278	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17261845	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17261859	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1820969	1.00[ASN][1000 genomes]
rs1864552	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1864554	1.00[ASN][1000 genomes]
rs2052954	1.00[ASN][1000 genomes]
rs2069895	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069898	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069902	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069904	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069919	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163345	1.00[ASN][1000 genomes]
rs2163348	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2460106	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2679409	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2896979	1.00[ASN][1000 genomes]
rs334137	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334138	1.00[ASN][1000 genomes]
rs334143	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334144	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334151	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334152	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334156	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334157	1.00[ASN][1000 genomes]
rs334158	1.00[ASN][1000 genomes]
rs334159	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs334160	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3732209	0.93[MEX][hapmap]
rs3893897	1.00[ASN][1000 genomes]
rs3958415	1.00[ASN][1000 genomes]
rs41280570	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4150400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150402	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150416	1.00[ASN][1000 genomes]
rs4150471	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150499	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4150523	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4536600	0.86[MEX][hapmap]
rs4662713	1.00[ASN][1000 genomes]
rs4662718	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4662719	1.00[ASN][1000 genomes]
rs4662720	1.00[ASN][1000 genomes]
rs4662736	1.00[ASN][1000 genomes]
rs55998444	1.00[ASN][1000 genomes]
rs56273408	1.00[ASN][1000 genomes]
rs59378658	1.00[ASN][1000 genomes]
rs61422716	1.00[ASN][1000 genomes]
rs6430933	1.00[ASN][1000 genomes]
rs6430936	1.00[ASN][1000 genomes]
rs6430938	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733478	1.00[ASN][1000 genomes]
rs6738690	1.00[ASN][1000 genomes]
rs6753288	0.86[MEX][hapmap]
rs6755028	0.86[MEX][hapmap]
rs6756535	1.00[ASN][1000 genomes]
rs72845944	1.00[ASN][1000 genomes]
rs72845975	1.00[ASN][1000 genomes]
rs72845976	1.00[ASN][1000 genomes]
rs72845991	1.00[ASN][1000 genomes]
rs72845993	1.00[ASN][1000 genomes]
rs72845997	1.00[ASN][1000 genomes]
rs72846002	1.00[ASN][1000 genomes]
rs72848604	1.00[ASN][1000 genomes]
rs72848612	1.00[ASN][1000 genomes]
rs72848615	1.00[ASN][1000 genomes]
rs72848616	1.00[ASN][1000 genomes]
rs72848618	1.00[ASN][1000 genomes]
rs7556675	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7562428	1.00[ASN][1000 genomes]
rs7582598	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7590030	0.93[MEX][hapmap]
rs7599210	0.86[MEX][hapmap]
rs7607907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs777554	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs777569	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9287540	1.00[ASN][1000 genomes]

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	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5937	ERCC3	cis	parietal	SCAN
rs5937	ERCC3	cis	Esophagus Muscularis	GTEx
rs5937	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128180200-128186800	Strong transcription	Liver	Liver
2	chr2:128181000-128191000	Weak transcription	Aorta	Aorta
3	chr2:128181400-128185200	Weak transcription	Spleen	Spleen
4	chr2:128181400-128186200	Weak transcription	Esophagus	oesophagus
5	chr2:128181400-128194000	Weak transcription	Gastric	stomach
6	chr2:128181400-128195200	Weak transcription	Pancreas	Pancrea
7	chr2:128181400-128196000	Weak transcription	Lung	lung
8	chr2:128181400-128209800	Weak transcription	Right Atrium	heart
9	chr2:128181600-128185200	Weak transcription	Fetal Intestine Small	intestine
10	chr2:128181600-128187600	Strong transcription	HepG2	liver
11	chr2:128181600-128195000	Weak transcription	Fetal Intestine Large	intestine
12	chr2:128181600-128197200	Weak transcription	Brain Anterior Caudate	brain
13	chr2:128182600-128186200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:128182800-128189600	Weak transcription	A549	lung
15	chr2:128183000-128186000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:128183000-128197000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:128183800-128190800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:128184000-128187200	Strong transcription	Fetal Stomach	stomach
19	chr2:128184200-128190200	Weak transcription	Psoas Muscle	Psoas
20	chr2:128184400-128184800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:128184600-128184800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:128184600-128184800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:128184600-128190000	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:128184600-128191400	Weak transcription	Brain Inferior Temporal Lobe	brain

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