Variant report

Variant	rs12464341
Chromosome Location	chr2:40176595-40176596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10181331	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10200630	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10490338	0.89[ASN][1000 genomes]
rs10865160	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11124713	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11685420	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11888334	0.88[ASN][1000 genomes]
rs11889689	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11893312	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11902593	0.88[ASN][1000 genomes]
rs12712668	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712669	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12988439	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13418507	0.98[ASN][1000 genomes]
rs1476989	0.91[ASN][1000 genomes]
rs1476990	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1541561	0.90[ASN][1000 genomes]
rs17024636	0.92[ASN][1000 genomes]
rs17024711	0.85[EUR][1000 genomes]
rs1861259	0.91[EUR][1000 genomes]
rs2058626	0.91[EUR][1000 genomes]
rs2058636	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058637	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058638	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2058639	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2080298	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2215969	0.92[EUR][1000 genomes]
rs2373705	0.90[ASN][1000 genomes]
rs2373708	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373709	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2373787	0.90[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap]
rs2888639	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670299	0.96[ASN][1000 genomes]
rs4670994	0.96[ASN][1000 genomes]
rs4670995	0.96[ASN][1000 genomes]
rs56118530	0.90[ASN][1000 genomes]
rs57091596	0.96[ASN][1000 genomes]
rs58570175	0.93[ASN][1000 genomes]
rs58969983	0.90[ASN][1000 genomes]
rs59034193	0.90[ASN][1000 genomes]
rs59957738	0.93[ASN][1000 genomes]
rs60613668	0.93[ASN][1000 genomes]
rs62136383	0.87[EUR][1000 genomes]
rs62137255	0.90[ASN][1000 genomes]
rs6544273	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544274	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544275	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544277	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6725817	0.87[ASN][1000 genomes]
rs6735955	0.99[ASN][1000 genomes]
rs725374	0.96[ASN][1000 genomes]
rs733958	0.95[ASN][1000 genomes]
rs737589	0.95[ASN][1000 genomes]
rs7572755	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7584288	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs768271	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs917974	0.87[EUR][1000 genomes]
rs957117	0.88[EUR][1000 genomes]
rs979716	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs985455	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003896	chr2:40094081-40231585	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1010609	chr2:40107234-40231674	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv535652	chr2:40107234-40231674	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv998885	chr2:40123904-40182851	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv873893	chr2:40137942-40222206	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv873894	chr2:40139250-40198380	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873895	chr2:40139250-40207338	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873896	chr2:40139250-40208665	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv873897	chr2:40139250-40225253	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv869668	chr2:40141079-40249854	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1003920	chr2:40141776-40245464	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1000423	chr2:40143646-40245464	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv456385	chr2:40151882-40195548	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv581497	chr2:40151882-40195548	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv456396	chr2:40154844-40231282	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv581498	chr2:40154844-40231282	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv581499	chr2:40154844-40241868	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv873898	chr2:40156882-40246716	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv456407	chr2:40158363-40208665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv581500	chr2:40158363-40208665	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
22	nsv873899	chr2:40161168-40281964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1006550	chr2:40164769-40209936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	nsv1009532	chr2:40165606-40291224	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv535653	chr2:40165606-40291224	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12464341	DHX57	cis	parietal	SCAN
rs12464341	SRSF7	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40174400-40176600	Enhancers	Osteobl	bone
2	chr2:40174400-40177000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr2:40175800-40181200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:40176000-40176600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:40176000-40178200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:40176200-40195200	Weak transcription	HSMM	muscle
7	chr2:40176400-40181400	Weak transcription	NH-A	brain
8	chr2:40176400-40181800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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