Variant report

Variant	rs2149592
Chromosome Location	chr9:108229990-108229991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108228659..108231354-chr9:108233201..108235205,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10991660	0.81[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.80[AFR][1000 genomes]
rs10991682	0.81[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs11999966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12002748	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12004019	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12004886	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12342465	0.83[AFR][1000 genomes]
rs13362922	0.90[AFR][1000 genomes]
rs1808155	0.87[AFR][1000 genomes]
rs1854124	0.94[EUR][1000 genomes]
rs2149593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2417627	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41277781	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66820447	0.83[EUR][1000 genomes]
rs7033452	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs7034699	0.86[AFR][1000 genomes]
rs7034702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042000	0.83[EUR][1000 genomes]
rs7858616	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7867012	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs7870485	0.95[AFR][1000 genomes]
rs7872832	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.98[MKK][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs9657645	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9969773	0.84[AFR][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	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
5	nsv1050141	chr9:108219667-108317424	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:93 , 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	chr9:108212200-108234800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:108214600-108309800	Weak transcription	HUVEC	blood vessel
4	chr9:108220200-108243400	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:108220400-108237400	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:108220400-108252600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:108220600-108231000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr9:108220600-108237000	Weak transcription	Pancreas	Pancrea
9	chr9:108220600-108237400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:108220800-108237000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:108220800-108237600	Weak transcription	Aorta	Aorta
12	chr9:108221000-108233200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:108221000-108235400	Weak transcription	Gastric	stomach
14	chr9:108221000-108236200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:108221000-108237400	Weak transcription	Brain Substantia Nigra	brain
16	chr9:108221000-108257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:108221000-108257200	Weak transcription	Fetal Stomach	stomach
18	chr9:108221000-108266000	Weak transcription	NHEK	skin
19	chr9:108221000-108277200	Weak transcription	Left Ventricle	heart
20	chr9:108221200-108232800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr9:108221200-108235000	Weak transcription	Spleen	Spleen
22	chr9:108221400-108232200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:108221800-108236600	Weak transcription	Small Intestine	intestine
24	chr9:108221800-108238200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr9:108222000-108237600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:108222200-108237400	Weak transcription	Psoas Muscle	Psoas
27	chr9:108222200-108259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:108222200-108277000	Weak transcription	Ovary	ovary
29	chr9:108222400-108236800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr9:108222400-108242200	Weak transcription	Brain Anterior Caudate	brain
31	chr9:108222400-108259000	Weak transcription	HSMMtube	muscle
32	chr9:108222600-108311400	Weak transcription	Fetal Heart	heart
33	chr9:108223200-108252600	Weak transcription	K562	blood
34	chr9:108223600-108255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:108224800-108244000	Weak transcription	Fetal Brain Male	brain
36	chr9:108225000-108237000	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr9:108225000-108249200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr9:108225800-108233600	Strong transcription	A549	lung
39	chr9:108226400-108232200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:108226400-108232400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:108226400-108234800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:108226600-108233600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:108226600-108234000	Strong transcription	NHDF-Ad	bronchial
44	chr9:108226600-108235600	Strong transcription	HepG2	liver
45	chr9:108226800-108231800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:108226800-108235400	Strong transcription	HSMM	muscle
47	chr9:108227000-108230600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:108227000-108231200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr9:108227000-108231600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:108227000-108233600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links