Variant report

Variant	rs6545238
Chromosome Location	chr2:52053430-52053431
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10183053	0.86[ASN][1000 genomes]
rs11563077	0.86[ASN][1000 genomes]
rs11563257	0.98[ASN][1000 genomes]
rs1347496	0.99[ASN][1000 genomes]
rs1435798	0.99[ASN][1000 genomes]
rs17868262	0.98[ASN][1000 genomes]
rs2354984	0.88[ASN][1000 genomes]
rs7582429	0.92[ASN][1000 genomes]
rs7582514	0.99[ASN][1000 genomes]
rs988517	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1009513	chr2:51890060-52821980	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv874079	chr2:51935797-52083566	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv874080	chr2:51946163-52068507	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581914	chr2:51959258-52074452	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv431047	chr2:51961737-52263543	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv874081	chr2:51975932-52062108	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1013553	chr2:52010500-52471153	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv535712	chr2:52010500-52471153	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv874083	chr2:52024350-52094039	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv874084	chr2:52025123-52062108	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv874085	chr2:52025123-52068507	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv874086	chr2:52025123-52094467	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv874087	chr2:52030983-52060125	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv581915	chr2:52030983-52066351	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv457751	chr2:52040842-52060125	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv581916	chr2:52040842-52060125	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv874088	chr2:52042513-52062108	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv874089	chr2:52042513-52096257	Enhancers Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv457762	chr2:52045220-52065417	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv581917	chr2:52045220-52065417	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv457774	chr2:52048275-52065967	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv581918	chr2:52048275-52065967	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
25	nsv457785	chr2:52051069-52065162	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv581919	chr2:52051069-52065162	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv874090	chr2:52051069-52068507	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545238	MTIF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52051800-52054000	Enhancers	Hela-S3	cervix
2	chr2:52052800-52053800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:52053400-52054200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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