Variant report

Variant	rs9463078
Chromosome Location	chr6:45181340-45181341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45160972..45165246-chr6:45178939..45182549,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1023090	0.88[CEU][hapmap]
rs10948222	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs12199720	0.83[CEU][hapmap]
rs12204678	0.82[EUR][1000 genomes]
rs1321081	0.83[CEU][hapmap]
rs1324531	0.85[EUR][1000 genomes]
rs1329713	0.88[CEU][hapmap]
rs1555681	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2093901	0.93[EUR][1000 genomes]
rs2093903	0.93[EUR][1000 genomes]
rs2396373	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2396425	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs3749863	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4373351	0.87[CEU][hapmap]
rs4446571	0.84[CEU][hapmap]
rs4506035	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4510673	0.83[CEU][hapmap]
rs4631280	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6458419	0.88[CEU][hapmap]
rs6458420	0.82[EUR][1000 genomes]
rs6458428	0.94[EUR][1000 genomes]
rs6899845	0.87[CEU][hapmap]
rs6937317	0.88[EUR][1000 genomes]
rs7451423	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7743116	0.85[EUR][1000 genomes]
rs9296453	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9349315	0.92[EUR][1000 genomes]
rs9357469	0.88[CEU][hapmap]
rs9357470	0.88[CEU][hapmap]
rs9357471	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9357478	0.91[EUR][1000 genomes]
rs9357480	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs9357484	0.83[CEU][hapmap]
rs9369558	0.83[CEU][hapmap]
rs9381359	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9381366	0.81[EUR][1000 genomes]
rs9381377	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9395066	0.96[CEU][hapmap]
rs9395069	0.85[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9395079	0.89[EUR][1000 genomes]
rs9395084	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9395086	0.83[EUR][1000 genomes]
rs9395087	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9395095	0.84[CEU][hapmap]
rs9463081	0.91[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1032906	chr6:45069368-45212863	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1028068	chr6:45169010-45246577	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9463078	SUPT3H	cis	multi-tissue	Pritchard
rs9463078	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45178200-45182200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:45179800-45182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:45179800-45182600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:45180000-45182000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:45180000-45182000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr6:45180000-45182600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr6:45180200-45181400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:45180200-45182400	Enhancers	Dnd41	blood
9	chr6:45180200-45182800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:45180400-45181400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr6:45181000-45182400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:45181000-45182600	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links