Variant report

Variant	rs13100490
Chromosome Location	chr3:99621726-99621727
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	chr3:99618971..99621795-chr3:99720299..99722726,2	MCF-7	breast:
2	chr3:99616272..99618855-chr3:99619104..99622005,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs13060898	1.00[JPT][hapmap]
rs13063594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13073356	1.00[JPT][hapmap]
rs13074107	1.00[JPT][hapmap]
rs13076199	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13081855	1.00[JPT][hapmap]
rs13082013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13084413	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13089461	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13095282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13096116	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097830	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17778253	1.00[JPT][hapmap]
rs34174004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34571898	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35098023	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36077012	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62283538	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788894	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6791889	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626245	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7636514	1.00[JPT][hapmap]
rs7647466	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7649862	1.00[JPT][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99616000-99631200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:99616600-99622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:99617200-99623200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:99619400-99623000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
8	chr3:99619800-99626600	Weak transcription	Psoas Muscle	Psoas
9	chr3:99620000-99624200	Enhancers	Hela-S3	cervix
10	chr3:99620000-99624800	Enhancers	NHDF-Ad	bronchial
11	chr3:99620000-99629800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:99620000-99638600	Weak transcription	Small Intestine	intestine
13	chr3:99620200-99621800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:99620200-99621800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:99620600-99622000	Enhancers	HepG2	liver
16	chr3:99620600-99623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:99620600-99624600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:99620800-99621800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:99620800-99622000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:99620800-99622000	Enhancers	HUVEC	blood vessel
21	chr3:99620800-99622000	Enhancers	NH-A	brain
22	chr3:99620800-99628400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:99620800-99628600	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:99621000-99621800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:99621000-99624000	Weak transcription	Adipose Nuclei	Adipose
26	chr3:99621200-99622000	Flanking Active TSS	HMEC	breast
27	chr3:99621200-99626600	Weak transcription	HSMMtube	muscle
28	chr3:99621200-99628000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:99621200-99638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:99621400-99622600	Weak transcription	Brain Anterior Caudate	brain
31	chr3:99621400-99622800	Weak transcription	A549	lung
32	chr3:99621400-99624800	Weak transcription	Liver	Liver
33	chr3:99621400-99626400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:99621400-99626800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:99621400-99627200	Weak transcription	Stomach Mucosa	stomach
36	chr3:99621400-99628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:99621400-99628600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:99621400-99629800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:99621600-99621800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:99621600-99621800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr3:99621600-99622600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:99621600-99623200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:99621600-99623200	Enhancers	NHEK	skin
44	chr3:99621600-99623600	Weak transcription	Osteobl	bone
45	chr3:99621600-99628600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links