Variant report

Variant	rs7558600
Chromosome Location	chr2:77083510-77083511
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10165732	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10170973	0.95[CHB][hapmap]
rs10176768	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10183619	0.86[CHB][hapmap]
rs10186912	0.86[CHB][hapmap]
rs10189408	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190510	0.85[CHB][hapmap]
rs10191141	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs10193309	0.86[CHB][hapmap]
rs10196177	0.82[ASW][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10196758	0.83[CHB][hapmap]
rs10196801	0.86[CHB][hapmap]
rs10196895	0.84[CHB][hapmap]
rs10196939	0.86[CHB][hapmap]
rs10520168	0.85[CEU][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs11126573	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs13385519	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13385839	0.91[CEU][hapmap]
rs13393238	0.91[CEU][hapmap]
rs13416719	0.89[CEU][hapmap]
rs13423635	0.91[CEU][hapmap]
rs13427514	0.83[CHB][hapmap]
rs1400847	0.91[CEU][hapmap];0.82[TSI][hapmap]
rs1446724	0.86[CHB][hapmap]
rs1446725	0.86[CHB][hapmap]
rs1470504	0.86[CHB][hapmap]
rs1470505	0.85[CHB][hapmap]
rs1470506	0.93[CHB][hapmap]
rs1470508	0.86[CHB][hapmap]
rs1584235	0.85[CHB][hapmap]
rs1584237	0.86[CHB][hapmap]
rs1596913	0.86[CHB][hapmap]
rs17013234	0.80[MEX][hapmap]
rs17013276	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs17013296	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[GIH][hapmap]
rs17013340	0.91[CEU][hapmap]
rs17013455	0.86[CEU][hapmap]
rs1829289	0.91[CEU][hapmap]
rs1921627	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap]
rs1929448	0.81[EUR][1000 genomes]
rs1929452	0.91[CEU][hapmap]
rs2020235	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065375	0.91[CEU][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap]
rs2121410	0.86[CHB][hapmap]
rs2121411	0.85[CHB][hapmap]
rs2178574	0.95[CEU][hapmap]
rs4277549	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4324338	0.84[CHB][hapmap]
rs4331533	0.91[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs4340548	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4853278	0.84[MEX][hapmap]
rs56270055	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6736181	0.91[CEU][hapmap];0.83[MEX][hapmap]
rs6740369	0.83[EUR][1000 genomes]
rs67475248	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6750897	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6751097	0.91[CEU][hapmap]
rs721390	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7580390	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7592470	0.91[CEU][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap]
rs7592608	0.91[CEU][hapmap]
rs7601256	0.81[CHB][hapmap]
rs7602571	0.82[ASN][1000 genomes]
rs7603852	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7604637	0.86[CEU][hapmap]
rs7607019	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs953854	0.91[CEU][hapmap]
rs985750	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005091	chr2:77009508-77112403	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1006086	chr2:77031163-77128651	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv874321	chr2:77031247-77113949	Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv874322	chr2:77031247-77209750	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1007648	chr2:77034405-77128651	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2752990	chr2:77038541-77217310	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv874323	chr2:77048896-77113949	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv874324	chr2:77048896-77201916	Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv874325	chr2:77053916-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv458274	chr2:77055883-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv582250	chr2:77055883-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv874326	chr2:77055883-77148261	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv582251	chr2:77055883-77154515	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7558600	C2orf3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77076200-77088600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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