Variant report

Variant	rs2787369
Chromosome Location	chr9:103048349-103048350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 183 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:180)

rs_ID	r²[population]
rs10116798	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10117150	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10117799	0.97[ASN][1000 genomes]
rs10118398	0.87[ASN][1000 genomes]
rs10118701	0.86[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs10120244	0.85[ASN][1000 genomes]
rs10123866	0.97[ASN][1000 genomes]
rs10123913	0.97[ASN][1000 genomes]
rs10124133	0.87[ASN][1000 genomes]
rs10124893	0.95[ASN][1000 genomes]
rs10125785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1014652	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10739796	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760720	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10760724	0.95[ASN][1000 genomes]
rs10819737	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10819751	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10819756	0.82[ASN][1000 genomes]
rs10819759	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10819761	0.90[ASN][1000 genomes]
rs10819762	0.87[ASN][1000 genomes]
rs10819764	0.87[ASN][1000 genomes]
rs10819767	0.87[ASN][1000 genomes]
rs10988973	0.85[JPT][hapmap]
rs10989009	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10989049	0.98[ASN][1000 genomes]
rs10989056	0.88[ASN][1000 genomes]
rs10989064	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989067	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10989070	0.87[ASN][1000 genomes]
rs1099909	0.82[AMR][1000 genomes]
rs11789196	0.97[ASN][1000 genomes]
rs12336751	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12552646	0.85[JPT][hapmap]
rs12684939	0.87[ASN][1000 genomes]
rs13301295	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1338119	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1338121	0.83[ASN][1000 genomes]
rs1338123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1338124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1338125	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1338126	0.83[ASN][1000 genomes]
rs1415926	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1534726	0.93[CEU][hapmap]
rs1535667	0.85[JPT][hapmap]
rs1930243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1961367	0.88[ASN][1000 genomes]
rs2026999	0.87[ASN][1000 genomes]
rs2057476	0.85[JPT][hapmap]
rs2065997	0.88[ASN][1000 genomes]
rs2151131	1.00[CHB][hapmap]
rs2210498	0.87[ASN][1000 genomes]
rs2245216	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2417084	0.87[ASN][1000 genomes]
rs2417176	0.87[ASN][1000 genomes]
rs2476441	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2476442	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2485745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2491095	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2491098	0.80[ASN][1000 genomes]
rs2761056	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2787361	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2787363	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2787364	0.85[JPT][hapmap]
rs2787365	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2787366	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2787368	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2787370	0.92[ASN][1000 genomes]
rs2787371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2787372	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787373	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787374	0.85[ASN][1000 genomes]
rs2787375	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787376	0.90[ASN][1000 genomes]
rs2787377	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2787379	0.86[ASN][1000 genomes]
rs2787380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2787382	0.83[ASN][1000 genomes]
rs2787383	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2787384	0.83[ASN][1000 genomes]
rs2787385	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2787386	0.80[ASN][1000 genomes]
rs2787388	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2787390	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2787391	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs2787394	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs2787395	1.00[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2787396	0.85[JPT][hapmap]
rs2787397	0.89[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2806682	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2806683	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2806684	0.84[CEU][hapmap]
rs2806687	0.85[JPT][hapmap]
rs2806689	0.83[ASN][1000 genomes]
rs2806690	0.81[ASN][1000 genomes]
rs2806691	0.83[ASN][1000 genomes]
rs2806692	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2806693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2806694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2806695	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2806696	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2806699	0.85[ASN][1000 genomes]
rs2806700	1.00[CHB][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2806702	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2806703	0.85[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs28464821	0.90[ASN][1000 genomes]
rs3813712	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3923501	0.98[ASN][1000 genomes]
rs4128230	0.95[ASN][1000 genomes]
rs4237194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4237195	0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4237196	0.88[ASN][1000 genomes]
rs4446782	0.98[ASN][1000 genomes]
rs4742782	0.97[ASN][1000 genomes]
rs4742783	0.92[ASN][1000 genomes]
rs4742784	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4743392	0.98[ASN][1000 genomes]
rs4743393	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743394	0.90[ASN][1000 genomes]
rs4743395	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4743396	0.87[ASN][1000 genomes]
rs5029342	0.97[ASN][1000 genomes]
rs5029343	0.98[ASN][1000 genomes]
rs59242794	0.90[ASN][1000 genomes]
rs6479001	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs6479002	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs6479008	0.93[ASN][1000 genomes]
rs6479009	0.98[ASN][1000 genomes]
rs6479011	0.87[ASN][1000 genomes]
rs6479013	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6479014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7020988	0.98[ASN][1000 genomes]
rs7021310	0.88[ASN][1000 genomes]
rs7025891	0.87[ASN][1000 genomes]
rs7025938	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7035619	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7036570	0.88[ASN][1000 genomes]
rs7047694	0.81[ASN][1000 genomes]
rs7048601	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs7472	0.97[ASN][1000 genomes]
rs7846794	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs7847213	0.93[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs7849966	0.98[ASN][1000 genomes]
rs7852189	0.87[ASN][1000 genomes]
rs7854693	0.97[ASN][1000 genomes]
rs7859492	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7860513	0.88[ASN][1000 genomes]
rs7861003	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7864494	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7866850	0.88[ASN][1000 genomes]
rs7869985	0.88[ASN][1000 genomes]
rs7871702	0.88[ASN][1000 genomes]
rs7874900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7875775	0.88[ASN][1000 genomes]
rs846751	0.86[AMR][1000 genomes]
rs846752	0.86[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs846753	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs846756	0.92[CEU][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs846759	0.85[JPT][hapmap]
rs846761	0.96[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs846765	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs846766	0.85[JPT][hapmap]
rs846768	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs846769	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs846770	0.96[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs860171	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs914711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9299337	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9299338	0.87[ASN][1000 genomes]
rs9408995	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9408998	0.84[ASN][1000 genomes]
rs9409325	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs944710	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs946054	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs959893	0.92[ASN][1000 genomes]
rs9695692	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9775014	0.92[ASN][1000 genomes]
rs9775182	0.98[ASN][1000 genomes]
rs9886877	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2787369	INVS	cis	multi-tissue	Pritchard
rs2787369	STX17	cis	Esophagus Mucosa	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102973000-103053800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:102979400-103054600	Weak transcription	NHEK	skin
3	chr9:102987400-103054600	Weak transcription	Gastric	stomach
4	chr9:102997800-103054400	Weak transcription	Colonic Mucosa	Colon
5	chr9:103029000-103053600	Weak transcription	Hela-S3	cervix
6	chr9:103029200-103054600	Weak transcription	Brain Angular Gyrus	brain
7	chr9:103040400-103053000	Weak transcription	NHLF	lung
8	chr9:103040400-103058600	Weak transcription	NH-A	brain
9	chr9:103044000-103067800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:103044200-103048800	Strong transcription	Left Ventricle	heart
11	chr9:103044200-103071200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
13	chr9:103044800-103049600	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:103044800-103067800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr9:103045200-103053000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:103045800-103050800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:103045800-103051200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr9:103045800-103051200	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr9:103045800-103052000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:103045800-103052000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:103045800-103052200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:103046000-103048400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:103046000-103051200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:103046000-103051600	Strong transcription	Placenta	Placenta
25	chr9:103046000-103052000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr9:103046000-103052400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:103046000-103075400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr9:103046200-103048800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:103046200-103050400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr9:103046200-103050600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:103046200-103051600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr9:103046200-103060000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:103046200-103072800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:103046400-103048400	Strong transcription	Brain Germinal Matrix	brain
35	chr9:103046400-103050000	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr9:103046400-103050600	Strong transcription	Placenta Amnion	Placenta Amnion
37	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:103046600-103048400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:103046600-103048400	Strong transcription	Brain Cingulate Gyrus	brain
40	chr9:103046600-103049000	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr9:103046600-103050600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
42	chr9:103046600-103051000	ZNF genes & repeats	Fetal Muscle Leg	muscle
43	chr9:103046600-103051200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
45	chr9:103046800-103048400	ZNF genes & repeats	Fetal Lung	lung
46	chr9:103046800-103050600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:103046800-103050600	ZNF genes & repeats	A549	lung
48	chr9:103046800-103055400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr9:103047000-103049400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:103047000-103049400	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links