Variant report

Variant	rs9409321
Chromosome Location	chr9:98588886-98588887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98583596..98587083-chr9:98587311..98591492,4	MCF-7	breast:
2	chr9:98585623..98589276-chr9:98636803..98639212,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10121403	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10481647	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10739632	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10760675	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10760692	0.84[AMR][1000 genomes]
rs10818017	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10983622	0.87[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10983692	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10983739	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10983773	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10983818	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12004422	0.87[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12375861	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12553442	0.86[ASN][1000 genomes]
rs1410783	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1928253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2117432	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164156	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2164157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2770837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930253	0.88[AMR][1000 genomes]
rs4743458	0.84[AMR][1000 genomes]
rs583716	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs585223	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs591579	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs601916	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs615866	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs626264	0.84[AMR][1000 genomes]
rs631273	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs636456	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs640281	0.81[AMR][1000 genomes]
rs643815	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478984	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479036	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs676453	0.88[AMR][1000 genomes]
rs678244	0.80[CEU][hapmap]
rs680468	0.88[AMR][1000 genomes]
rs680754	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs683829	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs689627	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs689749	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs689820	0.80[CEU][hapmap];0.84[AMR][1000 genomes]
rs689871	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs689979	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs690222	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs690304	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690335	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690420	0.82[AMR][1000 genomes]
rs690455	0.88[AMR][1000 genomes]
rs690484	0.83[AMR][1000 genomes]
rs700963	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7024710	0.88[AMR][1000 genomes]
rs7868559	0.89[AMR][1000 genomes]
rs7874897	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs816671	0.92[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs816676	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816681	0.98[ASN][1000 genomes]
rs913408	0.88[AMR][1000 genomes]
rs9409322	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]

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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9409321	LINC00476	cis	lung	GTEx
rs9409321	LINC00476	cis	Artery Aorta	GTEx
rs9409321	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs9409321	LINC00476	cis	Nerve Tibial	GTEx
rs9409321	LINC00476	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98570400-98589200	Weak transcription	Left Ventricle	heart
2	chr9:98570400-98589200	Weak transcription	Right Ventricle	heart
3	chr9:98570400-98593200	Weak transcription	Gastric	stomach
4	chr9:98570400-98593800	Weak transcription	Right Atrium	heart
5	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
7	chr9:98581800-98593800	Weak transcription	Fetal Intestine Small	intestine
8	chr9:98585200-98593600	Weak transcription	Spleen	Spleen
9	chr9:98585800-98589200	Weak transcription	Lung	lung
10	chr9:98585800-98592200	Weak transcription	Ovary	ovary
11	chr9:98585800-98593200	Weak transcription	Fetal Stomach	stomach
12	chr9:98585800-98593200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:98586000-98593200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr9:98588000-98589000	Enhancers	GM12878-XiMat	blood
15	chr9:98588200-98589000	Enhancers	HUVEC	blood vessel
16	chr9:98588600-98589000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:98588800-98589200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr9:98588800-98589400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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