Variant report

Variant	rs12777300
Chromosome Location	chr10:96174571-96174572
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	chr10:96162368..96164918-chr10:96174079..96176855,3	K562	blood:
2	chr10:96173417..96176346-chr10:96177510..96181137,5	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11187949	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11591693	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11595478	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11598738	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12569637	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571306	0.80[EUR][1000 genomes]
rs12571659	0.89[EUR][1000 genomes]
rs12766721	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12769392	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12770064	0.89[EUR][1000 genomes]
rs12785198	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2031322	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2151952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2151953	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34320768	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34402112	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34560326	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35029271	0.89[AMR][1000 genomes]
rs35602247	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35765566	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61427801	0.94[AMR][1000 genomes]
rs7082105	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv1815355	chr10:96162545-96189900	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv1817623	chr10:96162545-96189900	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12777300	CYP2C19	cis	Esophagus Mucosa	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96163800-96184400	Weak transcription	Gastric	stomach
2	chr10:96164600-96180000	Weak transcription	Fetal Intestine Small	intestine
3	chr10:96164800-96182400	Weak transcription	Lung	lung
4	chr10:96164800-96188200	Weak transcription	Right Atrium	heart
5	chr10:96165400-96175800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:96165600-96180600	Weak transcription	Left Ventricle	heart
7	chr10:96167800-96175800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr10:96169400-96179200	Weak transcription	Pancreas	Pancrea
9	chr10:96169400-96183800	Weak transcription	HSMM	muscle
10	chr10:96170400-96175800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:96171600-96174800	Enhancers	Brain Cingulate Gyrus	brain
12	chr10:96171600-96188200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:96171800-96183200	Weak transcription	Psoas Muscle	Psoas
14	chr10:96171800-96198200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:96172600-96176800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr10:96172800-96175800	Weak transcription	Fetal Kidney	kidney
17	chr10:96173400-96175600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr10:96173400-96175800	Weak transcription	Brain Angular Gyrus	brain
19	chr10:96173400-96175800	Weak transcription	Brain Anterior Caudate	brain
20	chr10:96173400-96175800	Weak transcription	Ovary	ovary
21	chr10:96173400-96175800	Weak transcription	Stomach Mucosa	stomach
22	chr10:96173400-96176800	Weak transcription	Adipose Nuclei	Adipose
23	chr10:96173400-96182600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:96173400-96182600	Weak transcription	Osteobl	bone
25	chr10:96173400-96183000	Weak transcription	HSMMtube	muscle
26	chr10:96173400-96183400	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:96173400-96188400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:96173600-96190200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr10:96173800-96174800	Weak transcription	Brain Hippocampus Middle	brain
30	chr10:96173800-96176200	Weak transcription	Fetal Lung	lung
31	chr10:96173800-96183000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:96174200-96175800	Weak transcription	Brain Substantia Nigra	brain
33	chr10:96174200-96176600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr10:96174400-96174600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links