Variant report

Variant	rs2299495
Chromosome Location	chr7:126356967-126356968
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:126354910..126358134-chr7:126363262..126365444,3	K562	blood:
2	7:126085913-126088095..7:126352172-126357573	GM12878	blood:
3	chr7:126354910..126357333-chr7:126363262..126365444,2	K562	blood:

Variant related genes	Relation type
ENSG00000179603	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1008906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10275004	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10275020	0.91[CHB][hapmap]
rs10487452	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs1074728	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs11764888	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11765247	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs11765912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11767915	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs11767976	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs11770188	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs11773107	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1345211	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs1361982	0.82[CHB][hapmap]
rs1468157	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17149953	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs17150011	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs17150014	0.90[CHB][hapmap]
rs17610771	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs17612316	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs2157821	0.80[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.86[TSI][hapmap]
rs41463444	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs4731326	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap]
rs62477942	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62477944	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62477945	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62477947	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6467098	1.00[JPT][hapmap]
rs6953879	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7805288	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7805959	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9690442	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529300	chr7:125669493-126587858	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1032938	chr7:126067684-126587859	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv539119	chr7:126067684-126587859	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv889187	chr7:126219766-126478190	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1032108	chr7:126278349-126362592	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv971569	chr7:126354720-126359366	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2299495	RBM28	cis	parietal	SCAN
rs2299495	MEST	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:126342000-126367800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr7:126356400-126357200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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