Variant report

Variant	rs10875700
Chromosome Location	chr12:48310931-48310932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48305115..48307646-chr12:48309250..48311512,3	K562	blood:
2	chr12:48297696..48300495-chr12:48310304..48312931,2	MCF-7	breast:
3	chr12:48301680..48304083-chr12:48309800..48311806,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10747525	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783221	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs10875695	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875697	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875703	0.89[EUR][1000 genomes]
rs10875704	0.87[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10875706	0.84[EUR][1000 genomes]
rs10875707	0.84[EUR][1000 genomes]
rs10875708	0.87[CEU][hapmap];0.82[CHD][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10875709	0.84[EUR][1000 genomes]
rs11168302	0.96[YRI][hapmap]
rs11168303	0.93[YRI][hapmap]
rs11168304	0.95[YRI][hapmap]
rs11168307	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11168308	0.88[EUR][1000 genomes]
rs11168310	0.80[EUR][1000 genomes]
rs11168311	0.87[EUR][1000 genomes]
rs11168314	0.87[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11168315	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11168316	0.87[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11168318	0.87[CEU][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11168319	0.82[EUR][1000 genomes]
rs11168320	0.84[EUR][1000 genomes]
rs11568820	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11829292	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231071	0.80[AFR][1000 genomes]
rs12304114	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12316950	0.89[EUR][1000 genomes]
rs4077869	0.85[YRI][hapmap]
rs4237855	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs4254129	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334089	0.81[JPT][hapmap]
rs4402365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4411326	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs4442605	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4454781	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61920870	0.88[EUR][1000 genomes]
rs7136534	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7300088	0.88[EUR][1000 genomes]
rs7300301	0.88[EUR][1000 genomes]
rs7302038	0.89[YRI][hapmap]
rs7302235	0.84[ASN][1000 genomes]
rs7303966	1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs7305180	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308216	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7970314	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs7975675	0.83[EUR][1000 genomes]
rs7976091	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7979360	0.93[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10875700	AQP6	cis	cerebellum	SCAN
rs10875700	RAPGEF3	cis	parietal	SCAN
rs10875700	LASS5	cis	parietal	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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