Variant report

Variant	rs12623287
Chromosome Location	chr2:141863233-141863234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10048632	0.81[CHB][hapmap]
rs10084341	0.89[YRI][hapmap]
rs10186270	0.96[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs10195363	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10205320	0.96[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12468793	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12611512	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];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618109	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12691592	0.91[MEX][hapmap]
rs13391141	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16845213	0.86[MEX][hapmap]
rs16845267	0.95[MEX][hapmap]
rs16845474	0.96[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1882628	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1882630	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1882637	0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap]
rs1882640	0.92[CEU][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1882641	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1922690	0.87[CEU][hapmap]
rs1922692	0.86[CEU][hapmap]
rs2091808	0.88[CEU][hapmap]
rs3856356	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs4133302	0.96[CEU][hapmap]
rs4954875	0.95[MEX][hapmap]
rs4954882	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs66986873	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6746542	0.96[CEU][hapmap]
rs6750303	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7599578	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9287305	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9287307	0.84[CEU][hapmap]
rs9287309	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv583198	chr2:141510791-142150620	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv875212	chr2:141796109-141877201	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv875214	chr2:141800473-141866271	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv875215	chr2:141800473-141877201	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv875216	chr2:141800473-141905052	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv875217	chr2:141800473-141919943	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv875218	chr2:141800473-141925845	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1003799	chr2:141803314-142033675	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv875219	chr2:141803602-141877201	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv459563	chr2:141803602-141925075	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv583200	chr2:141803602-141925075	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv875220	chr2:141819422-141882963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv875221	chr2:141826948-141877201	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv875222	chr2:141826948-141887814	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv875223	chr2:141826948-141905052	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1009434	chr2:141832339-142156180	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv459574	chr2:141833621-141866271	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv583201	chr2:141833621-141866271	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv875224	chr2:141841920-141877201	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv875225	chr2:141841920-141919943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv875226	chr2:141841920-141921632	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv875227	chr2:141841920-141928275	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv875228	chr2:141841920-141949292	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv1005236	chr2:141860005-142047695	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	nsv535948	chr2:141860005-142047695	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12623287	NXPH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:141862800-141864000	Enhancers	Dnd41	blood
2	chr2:141862800-141864200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr2:141862800-141864400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:141863000-141863600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr2:141863000-141864400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:141863000-141864600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:141863000-141864600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr2:141863200-141866400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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