Variant report

Variant	rs10120860
Chromosome Location	chr9:19089293-19089294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10113939	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117076	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10124438	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12002212	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341699	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12349511	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1932450	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62563590	0.93[ASN][1000 genomes]
rs62563640	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563641	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563642	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62563643	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475278	1.00[JPT][hapmap]
rs6475289	1.00[CHB][hapmap]
rs7024953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7025416	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7033648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7038785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7041472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7043607	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7467294	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7847488	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7855439	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7860085	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7864679	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7866883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7869183	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869414	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv2764156	chr9:19076894-19097008	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
3	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr9:19056000-19096400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:19056000-19101200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:19056600-19094800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:19056600-19095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:19056600-19095400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:19056600-19096000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr9:19056800-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
18	chr9:19066400-19096600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:19066800-19100400	Weak transcription	Fetal Heart	heart
20	chr9:19066800-19100800	Weak transcription	Small Intestine	intestine
21	chr9:19068800-19096800	Strong transcription	Fetal Thymus	thymus
22	chr9:19070000-19089400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:19070400-19090600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:19071200-19101200	Weak transcription	Psoas Muscle	Psoas
25	chr9:19073600-19098400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:19074400-19094200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:19074400-19094600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr9:19075400-19091200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:19075600-19092000	Weak transcription	Fetal Kidney	kidney
30	chr9:19077200-19091000	Weak transcription	Pancreas	Pancrea
31	chr9:19077400-19089400	Weak transcription	Esophagus	oesophagus
32	chr9:19077400-19090600	Weak transcription	Brain Substantia Nigra	brain
33	chr9:19077400-19102200	Weak transcription	Gastric	stomach
34	chr9:19078000-19089400	Weak transcription	Right Ventricle	heart
35	chr9:19078000-19091000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:19078200-19091800	Weak transcription	Spleen	Spleen
37	chr9:19078800-19089800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:19079200-19092400	Strong transcription	A549	lung
39	chr9:19079200-19099600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:19079400-19096400	Strong transcription	Dnd41	blood
41	chr9:19079600-19089600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:19079600-19101200	Weak transcription	Ovary	ovary
43	chr9:19081400-19094800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr9:19081400-19097200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:19082200-19089400	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:19083000-19089600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr9:19083800-19094800	Strong transcription	Placenta	Placenta
48	chr9:19083800-19096200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr9:19084000-19090400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:19084000-19096400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links