Variant report

Variant	rs34002163
Chromosome Location	chr2:171608172-171608173
allele	C/T
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	chr2:171608140-171608393	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:171608144-171608450	Hela-S3	cervix:	n/a	n/a
3	HEY1	chr2:171608088-171608434	K562	blood:	n/a	chr2:171608235-171608250 chr2:171608241-171608256
4	POLR2A	chr2:171607945-171608315	MCF-7	breast:	n/a	n/a
5	POLR2A	chr2:171608017-171608297	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:171608150-171608440	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:171608142-171608389	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr2:171608113-171608465	U87	brain:	n/a	n/a
9	POLR2A	chr2:171608164-171608345	GM12891	blood:	n/a	n/a
10	HEY1	chr2:171608109-171608442	K562	blood:	n/a	chr2:171608235-171608250 chr2:171608241-171608256
11	TAF1	chr2:171608134-171608448	H1-hESC	embryonic stem cell:	n/a	n/a
12	POU2F2	chr2:171608172-171608334	GM12878	blood:	n/a	chr2:171608246-171608258
13	POLR2A	chr2:171608149-171608449	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr2:171608158-171608446	HepG2	liver:	n/a	n/a
15	TAF1	chr2:171608149-171608425	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:171608132-171608476	GM12891	blood:	n/a	n/a
17	TAF1	chr2:171608155-171608365	GM12891	blood:	n/a	n/a
18	FOSL2	chr2:171608050-171608419	HepG2	liver:	n/a	n/a
19	TCF12	chr2:171608164-171608333	GM12878	blood:	n/a	n/a
20	TAF1	chr2:171608169-171608337	GM12891	blood:	n/a	n/a
21	POLR2A	chr2:171607980-171608309	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:171607935-171608304	ProgFib	skin:	n/a	n/a
23	HEY1	chr2:171608134-171608745	HepG2	liver:	n/a	chr2:171608235-171608250 chr2:171608241-171608256
24	POLR2A	chr2:171608113-171608540	GM12892	blood:	n/a	n/a
25	POLR2A	chr2:171607941-171608330	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:171607919-171608522	GM12892	blood:	n/a	n/a
27	MYC	chr2:171608158-171608257	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:171608150-171608442	GM12878	blood:	n/a	n/a
29	HEY1	chr2:171608170-171608340	HepG2	liver:	n/a	chr2:171608235-171608250 chr2:171608241-171608256
30	POLR2A	chr2:171608116-171608501	GM12878	blood:	n/a	n/a
31	MYC	chr2:171608156-171608267	K562	blood:	n/a	n/a
32	POLR2A	chr2:171608164-171608394	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:171607970-171609692	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:171608166-171608426	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr2:171608171-171608338	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:171608131-171608486	GM12891	blood:	n/a	n/a
37	POLR2A	chr2:171608098-171608549	SK-N-MC	brain:	n/a	n/a
38	POLR2A	chr2:171607894-171608345	MCF-7	breast:	n/a	n/a
39	POLR2A	chr2:171607911-171608370	Gliobla	brain:	n/a	n/a
40	MYC	chr2:171608041-171608322	MCF-7	breast:	n/a	n/a
41	POLR2A	chr2:171608168-171608357	H1-hESC	embryonic stem cell:	n/a	n/a
42	JUND	chr2:171608159-171608334	HepG2	liver:	n/a	n/a
43	POLR2A	chr2:171608135-171608425	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr2:171608116-171608414	U87	brain:	n/a	n/a
45	TAF1	chr2:171608157-171608364	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr2:171607944-171608321	K562	blood:	n/a	n/a
47	POLR2A	chr2:171608130-171608355	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr2:171607917-171608350	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr2:171607892-171608698	Hela-S3	cervix:	n/a	n/a
50	TAF1	chr2:171608165-171608364	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
EIF2S2P4	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165379	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10175644	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10181282	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10194303	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930438	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11895153	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12612710	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12613472	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12619010	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12994793	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13028382	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362489	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1362490	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894919	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3749036	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3764915	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764916	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4132720	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433235	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6433238	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433246	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433247	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433248	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66833017	0.91[EUR][1000 genomes]
rs6711176	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6723611	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6726371	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6738022	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757195	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7580460	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7608979	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869954	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs953680	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs954321	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9973711	0.90[EUR][1000 genomes];0.92[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	nsv963746	chr2:171602620-171609432	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34002163	GAD1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171574000-171620800	Weak transcription	Pancreas	Pancrea

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