Variant report

Variant	rs149942
Chromosome Location	chr6:28001610-28001611
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	chr6:28000166-28002054	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27780572..27782800-chr6:28000600..28002491,2	K562	blood:

Variant related genes	Relation type
OR2W2P	TF binding region
ENSG00000182611	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1150666	0.81[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs12173797	0.84[EUR][1000 genomes]
rs1225716	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1233691	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs1233708	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap]
rs1340004	0.81[CHB][hapmap]
rs149878	0.85[EUR][1000 genomes]
rs149897	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];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149900	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149941	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149948	0.87[AFR][1000 genomes]
rs149955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149958	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149961	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149962	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149965	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149969	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149970	0.94[ASW][hapmap];0.87[CHB][hapmap];0.92[LWK][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs149972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149977	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149978	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs156734	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs156736	0.85[AFR][1000 genomes]
rs156738	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs156739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1631552	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs16893666	0.81[CHB][hapmap]
rs169431	0.83[EUR][1000 genomes]
rs172166	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs1770131	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs17711344	0.81[CHB][hapmap]
rs17711801	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs17774663	0.81[CHB][hapmap]
rs183244	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1853097	0.81[CHB][hapmap]
rs188105	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs1904840	0.81[CHB][hapmap]
rs1904841	0.81[CHB][hapmap]
rs1947862	0.81[CHB][hapmap]
rs200951	0.86[CEU][hapmap]
rs200988	0.86[CEU][hapmap]
rs202908	0.89[EUR][1000 genomes]
rs203876	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs203877	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs203882	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap]
rs203884	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs203890	0.92[ASW][hapmap];1.00[YRI][hapmap]
rs203893	0.81[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap]
rs2116984	0.80[YRI][hapmap]
rs2275508	0.81[CHB][hapmap]
rs2281588	0.81[CHB][hapmap]
rs2295594	0.81[CHB][hapmap]
rs2622319	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs3173443	0.81[CHB][hapmap]
rs34171748	0.85[AFR][1000 genomes]
rs3734573	0.81[CHB][hapmap]
rs3823180	0.81[CHB][hapmap]
rs464312	0.85[AFR][1000 genomes]
rs469227	0.85[AFR][1000 genomes]
rs4711165	0.81[CHB][hapmap]
rs4713135	0.81[CHB][hapmap]
rs4713137	0.81[CHB][hapmap]
rs4713142	0.81[CHB][hapmap]
rs4713143	0.81[CHB][hapmap]
rs4713144	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs4713145	0.81[CHB][hapmap]
rs4713148	0.81[CHB][hapmap]
rs4713152	0.81[CHB][hapmap]
rs510987	0.86[CEU][hapmap];0.85[GIH][hapmap]
rs536704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs6922063	0.81[CHB][hapmap]
rs6931858	0.81[CHB][hapmap]
rs6932109	0.81[CHB][hapmap]
rs6941992	0.81[CHB][hapmap]
rs7755442	0.81[CEU][hapmap]
rs868987	0.81[CHB][hapmap]
rs9283884	0.81[CHB][hapmap]
rs9295758	0.81[CHB][hapmap]
rs9295759	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs9295760	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs9295761	0.81[CHB][hapmap]
rs9348793	0.81[CHB][hapmap]
rs9348794	0.81[CHB][hapmap]
rs9348796	0.81[CHB][hapmap]
rs9368554	0.81[CHB][hapmap]
rs9368555	0.81[CHB][hapmap]
rs9380047	0.81[CHB][hapmap]
rs9380052	0.81[CHB][hapmap]
rs9380055	0.81[CHB][hapmap]
rs9380057	0.81[CHB][hapmap]
rs9380059	0.81[CHB][hapmap]
rs9393881	0.94[ASW][hapmap];0.81[CHB][hapmap];0.96[YRI][hapmap]
rs9393890	0.81[CHB][hapmap]
rs9393893	0.81[CHB][hapmap]
rs9393897	0.81[CHB][hapmap]
rs9461433	0.81[CHB][hapmap]
rs9461443	0.86[CEU][hapmap]
rs9468274	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs9468286	0.81[CHB][hapmap]
rs9468298	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1817841	chr6:27984907-28007435	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs149942	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149942	ZSCAN23	cis	cerebellum	SCAN
rs149942	ZNF323	cis	cerebellum	SCAN
rs149942	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs149942	ZKSCAN3	cis	parietal	SCAN
rs149942	OR2B7P	cis	Thyroid	GTEx
rs149942	ZNF165	cis	lymphoblastoid	seeQTL
rs149942	AL022393.7	cis	Muscle Skeletal	GTEx
rs149942	ZNF187	cis	cerebellum	SCAN
rs149942	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149942	ZNF204P	cis	parietal	SCAN
rs149942	AL022393.7	cis	Artery Tibial	GTEx
rs149942	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149942	OR2B6	cis	parietal	SCAN
rs149942	ZNF187	cis	parietal	SCAN
rs149942	ZNF192	cis	cerebellum	SCAN
rs149942	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149942	ZNF323	cis	parietal	SCAN
rs149942	AL022393.7	cis	Nerve Tibial	GTEx
rs149942	OR2B8P	cis	Thyroid	GTEx
rs149942	NKAPL	cis	parietal	SCAN
rs149942	ZKSCAN3	cis	cerebellum	SCAN
rs149942	ZNF192	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28001600-28001800	Bivalent Enhancer	K562	blood

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