Variant report

Variant	rs2320029
Chromosome Location	chr14:68182609-68182610
allele	A/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	JUND	chr14:68182189-68182725	K562	blood:	n/a	chr14:68182393-68182402 chr14:68182391-68182402 chr14:68182391-68182403
2	MAX	chr14:68182405-68182731	K562	blood:	n/a	n/a
3	CEBPB	chr14:68182294-68182693	K562	blood:	n/a	chr14:68182423-68182434 chr14:68182423-68182436 chr14:68182423-68182436 chr14:68182423-68182434
4	MYC	chr14:68182365-68182768	K562	blood:	n/a	n/a
5	RCOR1	chr14:68182421-68182653	K562	blood:	n/a	n/a
6	POLR2A	chr14:68182466-68182687	K562	blood:	n/a	n/a
7	EP300	chr14:68182460-68182711	K562	blood:	n/a	n/a
8	ARID3A	chr14:68182269-68182664	K562	blood:	n/a	n/a
9	EGR1	chr14:68182453-68182687	K562	blood:	n/a	n/a
10	MAX	chr14:68182482-68182680	K562	blood:	n/a	n/a
11	ZNF384	chr14:68182600-68183117	K562	blood:	n/a	n/a
12	MYC	chr14:68182384-68182780	K562	blood:	n/a	n/a
13	BHLHE40	chr14:68182601-68182629	K562	blood:	n/a	n/a
14	CEBPB	chr14:68182270-68182646	K562	blood:	n/a	chr14:68182423-68182434 chr14:68182423-68182436 chr14:68182423-68182436 chr14:68182286-68182299 chr14:68182423-68182434
15	TBP	chr14:68182441-68182700	K562	blood:	n/a	n/a
16	RCOR1	chr14:68182428-68182789	K562	blood:	n/a	n/a
17	CUX1	chr14:68182398-68182629	K562	blood:	n/a	n/a
18	MAZ	chr14:68182446-68182715	K562	blood:	n/a	n/a
19	E2F6	chr14:68182509-68182666	K562	blood:	n/a	n/a
20	MAX	chr14:68182424-68182767	K562	blood:	n/a	n/a
21	TAL1	chr14:68182373-68182789	K562	blood:	n/a	chr14:68182601-68182619
22	CEBPB	chr14:68182140-68182628	Hela-S3	cervix:	n/a	chr14:68182423-68182434 chr14:68182423-68182436 chr14:68182423-68182436 chr14:68182286-68182299 chr14:68182423-68182434
23	JUND	chr14:68182106-68182659	SK-N-SH	brain:	n/a	chr14:68182393-68182402 chr14:68182391-68182402 chr14:68182391-68182403

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:68181892..68184033-chr14:68190366..68192082,2	K562	blood:
2	chr14:68181604..68183336-chr14:68184866..68187768,3	K562	blood:

Variant related genes	Relation type
RDH12	TF binding region
ENSG00000139988	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10459532	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1059238	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1120877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11620761	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11622441	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11623700	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11623711	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11623785	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624498	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11625839	0.80[EUR][1000 genomes]
rs11627201	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628860	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12050393	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1555193	0.86[ASW][hapmap];0.92[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];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17104490	0.95[GIH][hapmap]
rs17104526	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17104544	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17104550	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17104597	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17104621	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17249472	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17852293	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1955469	0.81[MEX][hapmap]
rs1955472	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955473	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2234511	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28390085	0.83[EUR][1000 genomes]
rs28873201	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742880	0.92[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3742881	0.84[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3742882	0.81[MEX][hapmap];0.89[YRI][hapmap]
rs3742883	0.81[MEX][hapmap]
rs4899221	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4899222	0.95[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4902506	0.92[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902508	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4902511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55900323	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56244142	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60581344	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6573790	0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6573794	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6573795	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7140310	0.92[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs7142897	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7144076	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7144124	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7151205	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7152326	0.84[CEU][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs7155788	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7159889	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72723111	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72723115	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72723122	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72723126	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72723137	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72723144	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72723150	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72723152	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72723154	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72723155	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72723156	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723158	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723160	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723163	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72723166	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723167	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742865	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs761513	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs761514	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8009250	0.82[EUR][1000 genomes]
rs8013767	0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8017147	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8017326	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019831	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8020591	0.91[CEU][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs932475	0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902068	chr14:68083133-68204876	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1042536	chr14:68136913-68343198	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv542122	chr14:68136913-68343198	Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv521832	chr14:68141009-68204876	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2320029	ATP6V1D	cis	parietal	SCAN
rs2320029	ZBTB1	cis	cerebellum	SCAN
rs2320029	C14orf162	cis	parietal	SCAN
rs2320029	RDH11	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68180600-68183000	Weak transcription	HepG2	liver
2	chr14:68181600-68183200	Enhancers	K562	blood
3	chr14:68181800-68182800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:68181800-68183000	Enhancers	Placenta	Placenta
5	chr14:68182600-68186600	Weak transcription	Hela-S3	cervix
6	chr14:68182600-68187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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