Variant report

Variant	rs12342071
Chromosome Location	chr9:108336148-108336149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108330989..108333120-chr9:108334347..108336541,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10991660	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap]
rs10991682	0.81[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs11999966	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12002748	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12004019	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12004886	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13362922	0.80[AFR][1000 genomes]
rs1808155	0.98[AFR][1000 genomes]
rs1854124	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2149592	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]
rs2149593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2417627	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41277781	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66820447	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7033452	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs7034699	0.96[AFR][1000 genomes]
rs7034702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042000	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7858616	0.95[AFR][1000 genomes];1.00[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];0.93[AFR][1000 genomes]
rs7870485	0.85[AFR][1000 genomes]
rs7872832	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[GIH][hapmap];0.98[MKK][hapmap];0.92[YRI][hapmap]
rs9657645	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049133	chr9:108292302-108356068	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108321600-108336800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:108321600-108336800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr9:108321600-108338000	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:108321600-108353600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:108321600-108354000	Weak transcription	Right Ventricle	heart
6	chr9:108321600-108360200	Weak transcription	HSMM	muscle
7	chr9:108321600-108397200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:108324800-108353800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr9:108325400-108337800	Weak transcription	Dnd41	blood
10	chr9:108325400-108339200	Weak transcription	Fetal Brain Male	brain
11	chr9:108325400-108357200	Weak transcription	A549	lung
12	chr9:108325600-108336600	Weak transcription	Fetal Lung	lung
13	chr9:108325600-108353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:108325600-108353200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:108325600-108353800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:108325800-108353800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:108326000-108338200	Weak transcription	Ovary	ovary
18	chr9:108328000-108372800	Weak transcription	NHEK	skin
19	chr9:108330800-108366200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:108331000-108337400	Weak transcription	Adipose Nuclei	Adipose
21	chr9:108331200-108340000	Weak transcription	NH-A	brain
22	chr9:108332800-108337200	Weak transcription	Osteobl	bone
23	chr9:108333200-108337800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:108333200-108338200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:108333200-108400400	Weak transcription	HMEC	breast
26	chr9:108333400-108336800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:108333400-108352600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr9:108333400-108352600	Weak transcription	Fetal Kidney	kidney
29	chr9:108333600-108337600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:108334000-108337200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:108334200-108368200	Weak transcription	Gastric	stomach
32	chr9:108334400-108336800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:108334600-108337800	Weak transcription	Fetal Intestine Large	intestine
34	chr9:108334600-108338400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:108334800-108337400	Weak transcription	Brain Anterior Caudate	brain
36	chr9:108334800-108353000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr9:108335000-108336600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:108335000-108336800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:108335000-108336800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:108335000-108337200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr9:108335000-108337400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr9:108335000-108338400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:108335000-108339800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:108335000-108352200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:108335000-108352600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr9:108335000-108352600	Weak transcription	Brain Hippocampus Middle	brain
47	chr9:108335000-108353000	Weak transcription	Aorta	Aorta
48	chr9:108335200-108336600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr9:108335200-108337000	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr9:108335200-108337200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links