Variant report

Variant	rs149945
Chromosome Location	chr6:28002853-28002854
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28001746..28003374-chr6:28020491..28023392,2	K562	blood:

Variant related genes	Relation type
ENSG00000182477	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1150666	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap]
rs12173797	0.84[EUR][1000 genomes]
rs1225716	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1233691	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs1233708	0.95[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs1340004	0.81[CHB][hapmap]
rs149878	0.85[EUR][1000 genomes]
rs149897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149900	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149942	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]
rs149944	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];0.97[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];0.97[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149961	0.83[CHB][hapmap];0.97[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	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs149970	0.87[CHB][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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149977	0.89[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	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs156736	0.86[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];0.97[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1631552	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs16893666	0.81[CHB][hapmap]
rs169431	0.83[EUR][1000 genomes]
rs172166	0.82[CHB][hapmap];0.96[YRI][hapmap]
rs1770131	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs17711344	0.81[CHB][hapmap]
rs17711801	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs17774663	0.83[CHB][hapmap]
rs183244	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[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];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs1904840	0.81[CHB][hapmap]
rs1904841	0.83[CHB][hapmap]
rs1947862	0.81[CHB][hapmap]
rs200951	0.86[CEU][hapmap]
rs200988	0.86[CEU][hapmap]
rs202908	0.89[EUR][1000 genomes]
rs203876	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs203877	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs203882	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs203884	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs203890	1.00[YRI][hapmap]
rs203893	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs2275508	0.81[CHB][hapmap]
rs2281588	0.83[CHB][hapmap]
rs2295594	0.83[CHB][hapmap]
rs2622319	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs3173443	0.81[CHB][hapmap]
rs34171748	0.86[AFR][1000 genomes]
rs3734573	0.83[CHB][hapmap]
rs3823180	0.81[CHB][hapmap]
rs464312	0.86[AFR][1000 genomes]
rs469227	0.86[AFR][1000 genomes]
rs4711165	0.81[CHB][hapmap]
rs4713135	0.81[CHB][hapmap]
rs4713137	0.83[CHB][hapmap]
rs4713142	0.81[CHB][hapmap]
rs4713143	0.83[CHB][hapmap]
rs4713144	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs4713145	0.81[CHB][hapmap]
rs4713148	0.83[CHB][hapmap]
rs4713152	0.81[CHB][hapmap]
rs510987	0.86[CEU][hapmap]
rs536704	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs6922063	0.81[CHB][hapmap]
rs6931858	0.81[CHB][hapmap]
rs6932109	0.81[CHB][hapmap]
rs6941992	0.81[CHB][hapmap]
rs7755442	0.82[CEU][hapmap]
rs868987	0.81[CHB][hapmap]
rs9283884	0.81[CHB][hapmap]
rs9295758	0.83[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	0.83[CHB][hapmap]
rs9348796	0.81[CHB][hapmap]
rs9368553	0.80[CHB][hapmap]
rs9368554	0.81[CHB][hapmap]
rs9368555	0.81[CHB][hapmap]
rs9380047	0.81[CHB][hapmap]
rs9380052	0.81[CHB][hapmap]
rs9380055	0.83[CHB][hapmap]
rs9380057	0.81[CHB][hapmap]
rs9380059	0.81[CHB][hapmap]
rs9393881	0.81[CHB][hapmap];0.96[YRI][hapmap]
rs9393890	0.83[CHB][hapmap]
rs9393893	0.83[CHB][hapmap]
rs9393897	0.81[CHB][hapmap]
rs9393901	0.81[CHB][hapmap]
rs9461433	0.83[CHB][hapmap]
rs9461443	0.87[CEU][hapmap]
rs9468274	0.81[CHB][hapmap];1.00[YRI][hapmap]
rs9468286	0.83[CHB][hapmap]
rs9468298	0.87[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs149945	ZNF323	cis	Cerebellum	GTEx
rs149945	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149945	ZNF323	cis	Frontal Cortex	GTEx
rs149945	AL022393.7	cis	Artery Tibial	GTEx
rs149945	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149945	AL022393.7	cis	Nerve Tibial	GTEx
rs149945	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149945	OR2B7P	cis	Thyroid	GTEx
rs149945	ZNF165	Cis_1M	lymphoblastoid	RTeQTL
rs149945	AL022393.7	cis	Muscle Skeletal	GTEx
rs149945	ZNF323	cis	Temporal Cortex	GTEx
rs149945	OR2B8P	cis	Thyroid	GTEx
rs149945	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149945	ZNF323	cis	Brain Pons	GTEx
rs149945	RP5-874C20.3	cis	Nerve Tibial	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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