Variant report

Variant	rs12487173
Chromosome Location	chr3:99494722-99494723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1038295	0.81[EUR][1000 genomes]
rs12491153	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12493124	1.00[AFR][1000 genomes]
rs1492343	0.82[EUR][1000 genomes]
rs4928222	0.82[EUR][1000 genomes]
rs55874130	1.00[AFR][1000 genomes]
rs55881709	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56140081	1.00[AFR][1000 genomes]
rs6789694	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73150300	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73860464	0.81[EUR][1000 genomes]
rs7635633	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][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	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	esv3463437	chr3:99491122-99495551	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription	n/a	n/a	inside rSNPs	n/a
6	esv3463438	chr3:99491122-99495551	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	n/a	n/a	inside rSNPs	n/a

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99462400-99495600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:99484400-99500400	Weak transcription	HSMMtube	muscle
3	chr3:99492000-99517600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:99493000-99496800	Enhancers	NHDF-Ad	bronchial
5	chr3:99493000-99497800	Genic enhancers	HSMM	muscle
6	chr3:99493200-99495000	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr3:99493200-99499400	Genic enhancers	Osteobl	bone
8	chr3:99493400-99495200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:99493600-99496000	Weak transcription	Placenta	Placenta
10	chr3:99493800-99495000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:99493800-99496000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:99494000-99494800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:99494000-99495200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:99494000-99499200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:99494200-99495000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:99494200-99495200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:99494200-99495200	Weak transcription	NH-A	brain
18	chr3:99494200-99495600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:99494200-99500400	Weak transcription	HMEC	breast
20	chr3:99494200-99513600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:99494400-99494800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:99494400-99495800	Enhancers	HUVEC	blood vessel
23	chr3:99494400-99498400	Weak transcription	Aorta	Aorta
24	chr3:99494600-99495000	Weak transcription	NHEK	skin
25	chr3:99494600-99496000	Enhancers	NHLF	lung
26	chr3:99494600-99500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links