Variant report

Variant	rs12821559
Chromosome Location	chr12:29542270-29542271
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr12:29542208-29542807	GM12891	blood:	n/a	chr12:29542468-29542480
2	POLR2A	chr12:29542145-29542876	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:29542165-29542449	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:29541771-29543691	GM12891	blood:	n/a	n/a
5	POLR2A	chr12:29542162-29542475	A549	lung:	n/a	n/a
6	HEY1	chr12:29542158-29542466	K562	blood:	n/a	n/a
7	POLR2A	chr12:29542108-29543774	GM12891	blood:	n/a	n/a
8	HEY1	chr12:29542131-29542484	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:29542174-29542455	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:29542096-29543012	GM12891	blood:	n/a	n/a
11	POLR2A	chr12:29542193-29542296	A549	lung:	n/a	n/a
12	YY1	chr12:29542202-29542894	GM12891	blood:	n/a	chr12:29542469-29542480 chr12:29542577-29542589 chr12:29542552-29542561
13	POLR2A	chr12:29542170-29542438	GM12878	blood:	n/a	n/a
14	GABPA	chr12:29542176-29542296	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:29542121-29543720	GM12891	blood:	n/a	n/a
16	HEY1	chr12:29542175-29542394	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:29542186-29542406	A549	lung:	n/a	n/a
18	POLR2A	chr12:29542209-29542324	K562	blood:	n/a	n/a
19	TAF1	chr12:29542127-29542828	GM12891	blood:	n/a	n/a
20	TAF1	chr12:29542116-29542481	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr12:29542192-29542417	A549	lung:	n/a	n/a
22	TAF1	chr12:29542144-29542467	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr12:29542270-29542369	Fibrobl	skin:	n/a	n/a
24	TAF1	chr12:29542210-29542893	GM12891	blood:	n/a	n/a
25	GABPA	chr12:29542172-29542393	HepG2	liver:	n/a	n/a
26	POLR2A	chr12:29542072-29542921	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:29542218-29542328	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:29542147-29542331	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr12:29542114-29543018	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:29542167-29542386	H1-hESC	embryonic stem cell:	n/a	n/a
31	HEY1	chr12:29542157-29542430	K562	blood:	n/a	n/a
32	POLR2A	chr12:29542162-29542466	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:29542095-29543788	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-677C1.2.1-2	chr12:29542227-29542786	NR_073172
2	lnc-RP11-677C1.2.1-2	chr12:29542227-29542786	NR_073170
3	lnc-RP11-677C1.2.1-2	chr12:29542227-29542786	NONHSAT027489

No data

Variant related genes	Relation type
OVCH1-AS1	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10492383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608616	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11609540	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11610197	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611687	0.81[EUR][1000 genomes]
rs11612172	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11613628	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615636	0.81[EUR][1000 genomes]
rs12809493	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810064	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12810315	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12811201	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12811723	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813520	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12813789	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12813996	0.81[EUR][1000 genomes]
rs12814180	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12814930	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12815222	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816511	0.80[EUR][1000 genomes]
rs12817163	0.80[EUR][1000 genomes]
rs12817578	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12817825	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12817985	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12819896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821498	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12821708	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12823372	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823422	0.81[EUR][1000 genomes]
rs12823485	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12823903	0.81[EUR][1000 genomes]
rs12824407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12829666	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830274	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12830493	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12830678	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830906	0.81[EUR][1000 genomes]
rs12831730	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832038	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832263	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1988943	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2350312	0.81[EUR][1000 genomes]
rs2882377	0.81[EUR][1000 genomes]
rs35618989	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636563	0.81[EUR][1000 genomes]
rs36126531	0.90[ASN][1000 genomes]
rs3764952	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67280216	0.81[EUR][1000 genomes]
rs7134744	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7295387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308372	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314594	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7961336	0.81[EUR][1000 genomes]
rs7964254	0.81[EUR][1000 genomes]
rs7979654	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv975466	chr12:29541892-29547802	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12821559	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12821559	RP11-996F15.2	cis	lung	GTEx
rs12821559	RP11-996F15.2	cis	Thyroid	GTEx
rs12821559	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12821559	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs12821559	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12821559	RP11-996F15.2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29535600-29542600	Weak transcription	Hela-S3	cervix
2	chr12:29535600-29543400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr12:29542200-29542800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr12:29542200-29542800	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr12:29542200-29543000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
6	chr12:29542200-29543600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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