Variant report

Variant	rs7846857
Chromosome Location	chr9:118043489-118043490
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	chr9:118041220..118043892-chr9:118094396..118096112,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1029341	0.82[EUR][1000 genomes]
rs10481680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817733	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs10817734	0.87[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10817741	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10817742	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10982619	0.85[JPT][hapmap]
rs10982621	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs10982654	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs12001569	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12338583	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12348813	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12683875	0.90[JPT][hapmap]
rs2183700	0.95[CHB][hapmap]
rs2285314	0.85[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2285315	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2418327	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989508	0.95[CHB][hapmap]
rs2989509	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2992142	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs2992144	0.95[CHB][hapmap]
rs35686252	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4112338	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap]
rs4147051	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72762372	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72762378	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72764238	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7846857	C1orf194	trans	brain	seeQTL
rs7846857	SLC47A2	trans	brain	seeQTL
rs7846857	ZMYND10	trans	brain	seeQTL
rs7846857	CAPS	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118038600-118044200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr9:118041000-118045200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:118041200-118045000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:118041200-118045000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:118042200-118043600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:118042800-118043600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr9:118042800-118052800	Weak transcription	Gastric	stomach
8	chr9:118043200-118045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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