Variant report

Variant	rs12006206
Chromosome Location	chr9:97390701-97390702
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97315886..97317442-chr9:97390408..97393191,2	MCF-7	breast:
2	chr9:97389746..97395320-chr9:97854192..97858136,7	MCF-7	breast:
3	chr2:70312789..70315252-chr9:97388486..97391200,2	MCF-7	breast:
4	chr9:97390244..97393079-chr9:97544131..97546613,2	MCF-7	breast:
5	chr9:97389422..97393205-chr9:97411609..97416128,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169564	Chromatin interaction
ENSG00000231806	Chromatin interaction
ENSG00000179818	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10993270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910850	0.86[CHB][hapmap];0.80[MEX][hapmap]
rs16910853	0.86[CHB][hapmap];0.80[MEX][hapmap]
rs16910860	0.86[CHB][hapmap]
rs2296707	0.81[CHB][hapmap]
rs4111369	0.86[CHB][hapmap];0.80[MEX][hapmap]
rs4129219	1.00[ASW][hapmap];1.00[CEU][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7028990	0.86[CHB][hapmap]
rs7859022	0.85[CHB][hapmap]
rs7859489	0.85[CHB][hapmap]
rs7872635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv614918	chr9:97380597-97412037	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv893597	chr9:97380597-97463435	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12006206	HIATL1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97371400-97401000	Weak transcription	Spleen	Spleen
2	chr9:97374600-97392600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:97374600-97393400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:97381400-97400400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr9:97381600-97401000	Weak transcription	Right Atrium	heart
6	chr9:97382600-97392800	Weak transcription	Lung	lung
7	chr9:97382600-97393000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:97382800-97399400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:97385800-97392800	Weak transcription	Fetal Lung	lung
10	chr9:97387600-97393200	Weak transcription	Fetal Stomach	stomach
11	chr9:97388400-97392600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr9:97389800-97390800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:97389800-97391000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr9:97389800-97391000	Enhancers	Gastric	stomach
15	chr9:97389800-97391200	Enhancers	Duodenum Mucosa	Duodenum
16	chr9:97389800-97393400	Enhancers	Liver	Liver
17	chr9:97390000-97394200	Enhancers	Stomach Mucosa	stomach
18	chr9:97390000-97397600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr9:97390200-97393200	Genic enhancers	Fetal Intestine Small	intestine
20	chr9:97390400-97390800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr9:97390400-97391000	Enhancers	Fetal Intestine Large	intestine
22	chr9:97390400-97391800	Weak transcription	Pancreas	Pancrea
23	chr9:97390400-97392600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr9:97390600-97392600	Weak transcription	Colonic Mucosa	Colon

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