Variant report

Variant	rs4510673
Chromosome Location	chr6:45350107-45350108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45344260..45347672-chr6:45348203..45354625,7	MCF-7	breast:
2	chr6:45349060..45350732-chr6:45362148..45364176,2	K562	blood:
3	chr6:45339593..45342500-chr6:45348795..45350804,2	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10948222	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10948231	0.89[ASN][1000 genomes]
rs12199720	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12205312	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12208924	0.86[CHD][hapmap]
rs12209727	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12525950	0.89[ASN][1000 genomes]
rs12529946	0.86[CHD][hapmap]
rs1285019	0.85[CHD][hapmap]
rs1321081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873345	0.81[CHD][hapmap]
rs17288334	1.00[ASN][1000 genomes]
rs2396425	0.94[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap]
rs2396502	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35565233	0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3749863	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs3923353	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4072928	0.89[CHD][hapmap]
rs4373351	1.00[CEU][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4446571	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4506035	0.80[EUR][1000 genomes]
rs62400336	1.00[ASN][1000 genomes]
rs6458441	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901786	0.89[CHD][hapmap]
rs6934594	0.96[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6935398	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6937317	0.85[AMR][1000 genomes]
rs717987	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7451423	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7740083	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7743116	0.81[AMR][1000 genomes]
rs7770401	0.88[EUR][1000 genomes]
rs9296453	0.92[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9296457	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9357478	0.81[AMR][1000 genomes]
rs9357480	0.92[CEU][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9357484	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9369552	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9369558	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9381373	0.89[CHD][hapmap]
rs9381383	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9395084	0.92[CEU][hapmap];0.95[TSI][hapmap]
rs9395086	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9395095	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9463076	0.89[CHD][hapmap]
rs9463078	0.83[CEU][hapmap]
rs9463081	0.94[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9463083	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9472451	0.89[CHD][hapmap]
rs9472453	0.81[CHD][hapmap]
rs9472460	0.81[EUR][1000 genomes]
rs988147	0.89[CHD][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4510673	SUPT3H	cis	cerebellum	SCAN
rs4510673	C6orf226	cis	cerebellum	SCAN
rs4510673	SUPT3H	cis	multi-tissue	Pritchard
rs4510673	SUPT3H	cis	lymphoblastoid	seeQTL
rs4510673	MAD2L1BP	cis	cerebellum	SCAN
rs4510673	CD2AP	cis	parietal	SCAN
rs4510673	SUPT3H	cis	parietal	SCAN
rs4510673	CYP39A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45346400-45351400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:45346600-45350200	Weak transcription	Right Atrium	heart
3	chr6:45347000-45355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:45347200-45354200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:45347400-45350600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:45349400-45351200	Enhancers	Placenta	Placenta
7	chr6:45349800-45350600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:45349800-45350800	Enhancers	Placenta Amnion	Placenta Amnion

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