Variant report

Variant	rs1568629
Chromosome Location	chr7:150239113-150239114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GIMAP6-3	chr7:150238842-150239186	NONHSAT124143

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1110093	0.93[EUR][1000 genomes]
rs11760959	0.96[EUR][1000 genomes]
rs11760960	0.96[EUR][1000 genomes]
rs11761391	0.82[EUR][1000 genomes]
rs11765395	0.96[EUR][1000 genomes]
rs11768988	0.96[EUR][1000 genomes]
rs11769223	0.96[EUR][1000 genomes]
rs11770957	0.96[EUR][1000 genomes]
rs11771561	0.85[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs11772952	0.96[EUR][1000 genomes]
rs11982681	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12672072	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12703078	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12703083	0.85[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs13222905	0.85[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs13224067	0.96[EUR][1000 genomes]
rs13231883	0.85[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs13232597	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs13240941	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13242186	0.85[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs1568627	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs1916003	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2177188	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2293172	0.85[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2293174	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs2373815	0.85[CEU][hapmap];0.94[EUR][1000 genomes]
rs34211617	0.96[EUR][1000 genomes]
rs34514106	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34545650	0.91[EUR][1000 genomes]
rs35133885	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35194540	0.96[EUR][1000 genomes]
rs35225135	0.82[EUR][1000 genomes]
rs35388682	0.96[EUR][1000 genomes]
rs35496043	0.96[EUR][1000 genomes]
rs35556724	0.83[EUR][1000 genomes]
rs35672177	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35677477	0.96[EUR][1000 genomes]
rs36021964	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36185661	0.87[EUR][1000 genomes]
rs3807378	0.91[EUR][1000 genomes]
rs4725345	0.96[EUR][1000 genomes]
rs4725348	0.83[EUR][1000 genomes]
rs4725905	0.85[CEU][hapmap]
rs4725908	0.98[EUR][1000 genomes]
rs4725921	0.92[EUR][1000 genomes]
rs4725923	0.85[EUR][1000 genomes]
rs58414124	0.98[EUR][1000 genomes]
rs62502270	0.93[EUR][1000 genomes]
rs62503177	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6949485	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73163503	0.93[EUR][1000 genomes]
rs7782113	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7802853	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803234	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809438	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1025129	chr7:150146593-150266217	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3395746	chr7:150181141-150300680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv3341786	chr7:150220353-150269134	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv437033	chr7:150228695-150245988	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2757243	chr7:150233827-150246984	ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv2759572	chr7:150233827-150246984	ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv3477570	chr7:150233916-150244133	ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv3477571	chr7:150233916-150244133	ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv438012	chr7:150234041-150239286	ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1568629	TMEM176B	cis	cerebellum	SCAN
rs1568629	GIMAP2	cis	cerebellum	SCAN
rs1568629	GIMAP4	cis	lymphoblastoid	seeQTL
rs1568629	ZNF425	cis	cerebellum	SCAN

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

No data

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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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