Variant report

Variant	rs10821462
Chromosome Location	chr9:98128647-98128648
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98122032..98123783-chr9:98127156..98129896,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1027710	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10739992	0.84[CEU][hapmap]
rs10761382	0.92[CEU][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10761387	0.89[EUR][1000 genomes]
rs10821455	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs10821458	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821459	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10821461	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10993518	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1979022	0.84[CEU][hapmap]
rs2031599	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs2036516	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2297596	0.84[CEU][hapmap]
rs2297597	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs35081772	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3737142	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs3844341	0.88[CEU][hapmap]
rs3852402	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs4647382	0.88[CEU][hapmap];0.86[MKK][hapmap]
rs4647459	0.84[CEU][hapmap]
rs4647462	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs4647475	0.88[CEU][hapmap]
rs4743993	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4744446	0.88[CEU][hapmap]
rs4744451	0.84[CEU][hapmap]
rs4744455	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4744459	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7026047	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7027204	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs7850958	0.84[CEU][hapmap]
rs7854570	0.88[CEU][hapmap];0.83[MKK][hapmap]
rs7858493	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs963774	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1045479	chr9:98115290-98172995	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10821462	HABP4	cis	cerebellum	SCAN
rs10821462	PHF2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98123400-98131000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98123600-98128800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:98125600-98129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:98125600-98129200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:98126000-98131800	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:98126000-98132000	Weak transcription	HSMMtube	muscle
7	chr9:98127400-98129200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:98127800-98129000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:98127800-98129000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:98127800-98129200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr9:98127800-98129400	Enhancers	Fetal Stomach	stomach
12	chr9:98127800-98129600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:98128000-98129000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:98128000-98139200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:98128200-98129200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:98128200-98129800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr9:98128400-98128800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:98128400-98129200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr9:98128600-98129200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links