Variant report

Variant	rs2771038
Chromosome Location	chr9:108219091-108219092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10761100	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10816278	0.89[AMR][1000 genomes]
rs10820809	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820810	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10820812	0.89[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10820813	0.96[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1327354	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1360089	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1806898	0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs1815383	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1960023	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1987634	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2225246	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2427769	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2518106	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2518112	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518114	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2518116	0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2518120	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2518123	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2518124	0.82[ASN][1000 genomes]
rs2518128	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2518131	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs2768279	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2768280	0.84[EUR][1000 genomes]
rs2768283	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2768290	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2768291	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2768292	0.82[ASN][1000 genomes]
rs2768294	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs2771041	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2771042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2812297	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2812303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2812307	0.90[ASN][1000 genomes]
rs2812308	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2812310	0.88[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4742650	0.83[AMR][1000 genomes]
rs4742947	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4742948	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6477449	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020083	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7357632	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[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	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1053973	chr9:108199177-108300186	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv615115	chr9:108205262-108298183	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893692	chr9:108218852-108320988	ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108211000-108248000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:108211200-108219800	Weak transcription	Lung	lung
3	chr9:108211200-108220000	Weak transcription	Left Ventricle	heart
4	chr9:108211200-108220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:108211200-108220400	Weak transcription	Primary B cells from cord blood	blood
6	chr9:108211200-108220600	Weak transcription	Ovary	ovary
7	chr9:108211400-108220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:108211400-108220000	Weak transcription	Right Ventricle	heart
9	chr9:108211400-108222000	Weak transcription	Stomach Mucosa	stomach
10	chr9:108211600-108219600	Weak transcription	Brain Substantia Nigra	brain
11	chr9:108211600-108220000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:108211800-108219600	Weak transcription	Brain Angular Gyrus	brain
13	chr9:108211800-108219800	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:108211800-108220000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr9:108211800-108227000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:108212200-108219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:108212200-108219600	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:108212200-108219800	Weak transcription	Brain Anterior Caudate	brain
19	chr9:108212200-108220000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:108212200-108220000	Weak transcription	Fetal Intestine Small	intestine
21	chr9:108212200-108220400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:108212200-108220600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:108212400-108219600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr9:108212400-108219800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:108212600-108220000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr9:108212600-108220000	Weak transcription	NHEK	skin
28	chr9:108212800-108219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:108212800-108220200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:108212800-108220200	Weak transcription	Hela-S3	cervix
31	chr9:108212800-108226600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:108213600-108219800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:108214000-108219200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:108214000-108219600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:108214000-108220000	Weak transcription	A549	lung
36	chr9:108214200-108220400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:108214400-108219200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr9:108214400-108219400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:108214400-108219800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr9:108214400-108220000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:108214400-108220000	Weak transcription	NHLF	lung
42	chr9:108214400-108221000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:108214400-108227200	Weak transcription	Fetal Kidney	kidney
44	chr9:108214600-108220000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:108214600-108220000	Weak transcription	Fetal Stomach	stomach
46	chr9:108214600-108221000	Weak transcription	Small Intestine	intestine
47	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
48	chr9:108214800-108219600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr9:108216800-108219400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr9:108217200-108220400	Weak transcription	HepG2	liver

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