Variant report

Variant	rs2009023
Chromosome Location	chr9:117800105-117800106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10123436	0.93[ASN][1000 genomes]
rs10759753	0.92[AFR][1000 genomes]
rs10817705	0.93[ASN][1000 genomes]
rs1330363	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1330364	0.92[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13321	0.82[JPT][hapmap]
rs1411456	0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1411461	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1537017	0.83[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1547691	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1547692	0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16932078	0.81[JPT][hapmap]
rs1854707	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1888222	0.83[ASN][1000 genomes]
rs2104772	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2210108	0.86[AFR][1000 genomes]
rs2297180	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs3789870	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3789872	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs3789873	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs4460459	0.83[JPT][hapmap]
rs6478127	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6478128	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7027148	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7030164	0.82[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7032224	0.86[AFR][1000 genomes]
rs7875852	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs944223	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs944226	0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs953288	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs955450	1.00[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv519131	chr9:117796986-117804667	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117773400-117803200	Weak transcription	Esophagus	oesophagus
2	chr9:117781800-117808600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
4	chr9:117789000-117808600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:117792000-117800400	Weak transcription	Fetal Lung	lung
7	chr9:117792000-117802600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:117793200-117800600	Weak transcription	Lung	lung
10	chr9:117793600-117802600	Weak transcription	Fetal Kidney	kidney
11	chr9:117794400-117800400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:117795200-117803400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:117796200-117801000	Enhancers	HMEC	breast
14	chr9:117796600-117800600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:117796600-117801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:117797200-117800800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:117797400-117807400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
18	chr9:117797800-117803400	Enhancers	Rectal Smooth Muscle	rectum
19	chr9:117798200-117800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:117798200-117805000	Weak transcription	HSMM	muscle
21	chr9:117798400-117800400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:117798600-117800200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:117798600-117801400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:117798600-117801800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:117798600-117801800	Weak transcription	Spleen	Spleen
26	chr9:117798600-117802400	Enhancers	Colon Smooth Muscle	Colon
27	chr9:117798600-117804200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:117798800-117800400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:117798800-117803600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:117798800-117804800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:117799000-117800200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:117799000-117800400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:117799200-117800200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:117799200-117800200	Weak transcription	Aorta	Aorta
35	chr9:117799200-117800400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:117799200-117800400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:117799200-117801600	Weak transcription	Brain Hippocampus Middle	brain
38	chr9:117799200-117801800	Weak transcription	Right Ventricle	heart
39	chr9:117799200-117805000	Weak transcription	HSMMtube	muscle
40	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:117799400-117800200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:117799400-117800400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:117799400-117800400	Weak transcription	NHDF-Ad	bronchial
44	chr9:117799400-117800400	Strong transcription	Osteobl	bone
45	chr9:117799400-117817000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr9:117799600-117800400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:117799600-117800400	Weak transcription	Fetal Muscle Leg	muscle
48	chr9:117799800-117800400	Weak transcription	NHLF	lung
49	chr9:117799800-117804600	Strong transcription	NHEK	skin
50	chr9:117800000-117800400	Weak transcription	Fetal Stomach	stomach

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