Variant report

Variant	rs1929395
Chromosome Location	chr9:117856912-117856913
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:117853634-117857758	U87	brain:	n/a	n/a
2	POLR2A	chr9:117851943-117857764	U87	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10982535	0.95[JPT][hapmap]
rs1250019	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1250021	0.81[JPT][hapmap]
rs1250022	0.82[JPT][hapmap]
rs1250023	0.88[CEU][hapmap]
rs1250026	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs1250027	0.95[JPT][hapmap]
rs1273108	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs1330349	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1330350	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1330356	0.95[JPT][hapmap]
rs1330360	0.93[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1360291	0.88[CEU][hapmap]
rs1511	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1755639	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1757100	0.89[CEU][hapmap]
rs1757106	0.89[JPT][hapmap]
rs1757107	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2183701	0.95[JPT][hapmap]
rs2274836	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2480930	0.85[ASN][1000 genomes]
rs2480932	0.95[JPT][hapmap]
rs2480933	0.95[JPT][hapmap]
rs2482078	0.88[CEU][hapmap];0.83[YRI][hapmap]
rs2482080	0.93[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2988578	0.93[CEU][hapmap];0.80[AMR][1000 genomes]
rs2989518	0.93[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs3789867	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3789868	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs769331	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs881496	0.95[JPT][hapmap]
rs944227	0.95[JPT][hapmap];0.86[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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
3	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
4	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:117849600-117857000	Weak transcription	Spleen	Spleen
6	chr9:117849600-117864600	Weak transcription	HMEC	breast
7	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
8	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:117850800-117857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:117852400-117857000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:117853400-117857000	Weak transcription	NHLF	lung
13	chr9:117853400-117857200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:117853400-117857200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:117853400-117858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:117853400-117861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:117854000-117860600	Weak transcription	NHDF-Ad	bronchial
19	chr9:117854400-117860600	Weak transcription	Osteobl	bone
20	chr9:117855000-117857000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr9:117855200-117857000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr9:117855200-117857200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr9:117855200-117857600	Enhancers	Rectal Smooth Muscle	rectum
24	chr9:117855200-117861000	Weak transcription	NH-A	brain
25	chr9:117855400-117857200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr9:117855400-117857400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr9:117855400-117857600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
28	chr9:117855600-117857200	Enhancers	Fetal Lung	lung
29	chr9:117855600-117857600	Enhancers	Colon Smooth Muscle	Colon
30	chr9:117855800-117857200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:117856200-117857200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:117856200-117857400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr9:117856400-117857000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:117856400-117857200	Enhancers	Brain Substantia Nigra	brain
35	chr9:117856400-117857400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr9:117856600-117857200	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr9:117856600-117857200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr9:117856600-117857400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
39	chr9:117856800-117857000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr9:117856800-117857200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:117856800-117857400	Genic enhancers	NHEK	skin
42	chr9:117856800-117860400	Weak transcription	Fetal Stomach	stomach

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