Variant report

Variant	rs9409513
Chromosome Location	chr9:97064989-97064990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97064666..97066438-chr9:97068084..97069601,2	K562	blood:
2	chr9:97057093..97059981-chr9:97063795..97065484,2	K562	blood:
3	chr9:97052305..97055569-chr9:97062185..97065091,3	K562	blood:
4	chr9:97062115..97063983-chr9:97064405..97066537,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10821325	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10821326	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12338655	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16912862	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1752786	0.85[CHB][hapmap]
rs1971396	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277182	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2479601	0.89[CEU][hapmap]
rs2479602	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2769119	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3118753	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3118754	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3118756	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3118761	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3118762	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3118765	0.82[AMR][1000 genomes]
rs3131899	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs3131901	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131902	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131904	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3131910	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4477096	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4744346	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs59717415	0.86[ASN][1000 genomes]
rs6479533	0.82[ASN][1000 genomes]
rs6479534	0.82[ASN][1000 genomes]
rs6479537	0.91[CHB][hapmap]
rs684892	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs688165	0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7025755	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs7031088	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7031496	0.89[CEU][hapmap]
rs7041842	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7848227	0.88[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7857240	0.83[ASN][1000 genomes]
rs9299422	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9409511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9409512	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409514	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9409718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409759	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap]
rs9409765	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9695176	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9696843	0.86[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes];0.82[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	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9409513	RP11-307E17.8	cis	Esophagus Muscularis	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:97041200-97065400	Weak transcription	Small Intestine	intestine
3	chr9:97042600-97068400	Weak transcription	Fetal Brain Female	brain
4	chr9:97043800-97066400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:97055600-97066600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:97055600-97067800	Weak transcription	HepG2	liver
7	chr9:97055600-97068000	Weak transcription	Pancreas	Pancrea
8	chr9:97058800-97065000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr9:97062800-97066200	Weak transcription	Fetal Brain Male	brain
10	chr9:97063000-97065200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:97063200-97065000	Weak transcription	Fetal Stomach	stomach
12	chr9:97063200-97066000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:97063400-97065000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:97063400-97065000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:97063400-97065000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:97063400-97065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:97063400-97065000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:97063400-97065000	Weak transcription	Left Ventricle	heart
19	chr9:97063400-97065000	Weak transcription	Ovary	ovary
20	chr9:97063400-97065000	Weak transcription	A549	lung
21	chr9:97063400-97065200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr9:97063400-97065200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:97063600-97065200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr9:97063600-97065200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:97063600-97065200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr9:97063600-97065200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:97063600-97065200	Weak transcription	Aorta	Aorta
28	chr9:97063600-97065200	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:97063600-97065200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:97063600-97065200	Weak transcription	Spleen	Spleen
31	chr9:97063600-97065200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr9:97063600-97065400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:97063600-97068200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:97063800-97065400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr9:97063800-97065400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:97064200-97067600	Weak transcription	Primary T cells from cord blood	blood
37	chr9:97064200-97068000	Weak transcription	Adipose Nuclei	Adipose
38	chr9:97064400-97065800	Enhancers	K562	blood
39	chr9:97064600-97065000	Enhancers	Stomach Mucosa	stomach
40	chr9:97064600-97066200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:97064800-97067400	Weak transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links