Variant report

Variant	rs3789875
Chromosome Location	chr9:117795288-117795289
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117794694..117797326-chr9:117797727..117800455,2	K562	blood:

Variant related genes	Relation type
ENSG00000041982	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10817701	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10982497	0.86[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10982503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982504	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982509	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs11788513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11792749	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12338715	0.87[ASN][1000 genomes]
rs12343737	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12344929	1.00[YRI][hapmap]
rs12346540	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12347433	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12348090	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12349585	0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs12351083	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13285041	0.83[ASN][1000 genomes]
rs13286217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1411453	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1411455	0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2274835	0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs2297179	0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2297181	0.93[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs28491824	0.88[ASN][1000 genomes]
rs34690752	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34865477	0.83[ASN][1000 genomes]
rs3789871	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap]
rs4452883	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66539628	0.82[ASN][1000 genomes]
rs7859478	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1840787	chr9:117787173-117803882	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv1826575	chr9:117787173-117805719	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3789875	TNFSF8	cis	parietal	SCAN
rs3789875	TXN	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117781800-117797400	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:117781800-117798200	Weak transcription	Fetal Intestine Large	intestine
4	chr9:117781800-117798400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
6	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
7	chr9:117783200-117796800	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:117786600-117796600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:117788000-117796600	Strong transcription	NH-A	brain
10	chr9:117788400-117797400	Weak transcription	Spleen	Spleen
11	chr9:117788800-117796600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:117789600-117797400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:117789800-117797400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:117790000-117797400	Strong transcription	NHDF-Ad	bronchial
16	chr9:117790200-117796200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:117791200-117796800	Strong transcription	NHLF	lung
18	chr9:117791600-117796600	Strong transcription	Fetal Stomach	stomach
19	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:117791800-117796400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:117791800-117797200	Weak transcription	HSMM	muscle
22	chr9:117791800-117797200	Strong transcription	NHEK	skin
23	chr9:117791800-117798000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:117792000-117800400	Weak transcription	Fetal Lung	lung
25	chr9:117792000-117802600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:117792600-117796000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr9:117792600-117798000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:117793200-117796200	Weak transcription	HMEC	breast
30	chr9:117793200-117800600	Weak transcription	Lung	lung
31	chr9:117793400-117796200	Weak transcription	Aorta	Aorta
32	chr9:117793600-117795800	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:117793600-117802600	Weak transcription	Fetal Kidney	kidney
34	chr9:117793800-117796000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:117794200-117797200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:117794400-117798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:117794400-117798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:117794400-117800400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr9:117794600-117795400	Enhancers	Fetal Heart	heart
40	chr9:117794600-117795800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:117794600-117796800	Genic enhancers	Colon Smooth Muscle	Colon
42	chr9:117794600-117799200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:117794800-117795400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:117794800-117797400	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:117794800-117798800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:117794800-117799400	Genic enhancers	Osteobl	bone
47	chr9:117795000-117796200	Genic enhancers	Stomach Smooth Muscle	stomach
48	chr9:117795200-117796600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:117795200-117797400	Weak transcription	HSMMtube	muscle
50	chr9:117795200-117798200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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