Variant report

Variant	rs10498760
Chromosome Location	chr6:45363796-45363797
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45352135..45354442-chr6:45361892..45364565,2	MCF-7	breast:
2	chr6:45349060..45350732-chr6:45362148..45364176,2	K562	blood:
3	chr6:45344688..45347304-chr6:45362865..45365385,2	MCF-7	breast:
4	chr6:45363391..45365276-chr6:45387477..45390341,2	MCF-7	breast:
5	chr6:45343263..45347310-chr6:45361550..45366697,4	K562	blood:
6	chr6:45344122..45347310-chr6:45361550..45366697,4	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction
ENSG00000271857	Chromatin interaction
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004130	1.00[ASW][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11498195	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11963804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966902	0.88[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11968177	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12529907	0.82[JPT][hapmap]
rs17209846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17209853	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17209874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17209881	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288376	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288397	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1977152	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3749864	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3792952	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3805811	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3805818	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3828722	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3828723	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4370348	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4413613	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4413614	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4714856	1.00[ASW][hapmap]
rs56789892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57013196	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58571027	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59397804	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61467394	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921145	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7751427	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7768466	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7768666	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7771980	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10498760	SUPT3H	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45356800-45382800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:45358400-45383000	Weak transcription	Osteobl	bone
3	chr6:45362200-45376200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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