Variant report

Variant	rs10873242
Chromosome Location	chr14:71233996-71233997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71232260..71234567-chr14:71236816..71239226,2	MCF-7	breast:
2	chr14:71233530..71235604-chr14:71275147..71277028,3	MCF-7	breast:
3	chr14:71233318..71235646-chr14:71241902..71243405,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006432	Chromatin interaction
ENSG00000259153	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1034769	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10873241	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12589737	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1476609	0.87[ASN][1000 genomes]
rs2107666	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2332455	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2332458	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3814872	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4899368	0.85[ASN][1000 genomes]
rs4899369	0.83[ASN][1000 genomes]
rs4902844	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4902852	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6573980	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7140653	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7152516	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8007131	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8011507	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8018294	0.89[AMR][1000 genomes];0.88[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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
2	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine
5	chr14:71216400-71238200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:71216600-71245800	Weak transcription	Brain Germinal Matrix	brain
7	chr14:71216800-71238400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr14:71220600-71238600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:71220800-71240400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
11	chr14:71221000-71237600	Weak transcription	Fetal Kidney	kidney
12	chr14:71221800-71239600	Weak transcription	Liver	Liver
13	chr14:71222200-71238000	Weak transcription	Esophagus	oesophagus
14	chr14:71222200-71238200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr14:71222200-71238200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr14:71222200-71258200	Weak transcription	HepG2	liver
17	chr14:71222400-71238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
19	chr14:71222800-71238200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
21	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:71223400-71240000	Weak transcription	Pancreas	Pancrea
23	chr14:71224000-71258000	Weak transcription	Dnd41	blood
24	chr14:71227600-71238000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:71227800-71235200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:71227800-71238000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr14:71227800-71238400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr14:71227800-71245200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr14:71227800-71245600	Weak transcription	Lung	lung
30	chr14:71227800-71257800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr14:71228000-71235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr14:71228000-71235200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr14:71228000-71236400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr14:71228000-71237800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr14:71228000-71238200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr14:71228000-71238200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:71228000-71238400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr14:71228000-71238400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:71228000-71242000	Weak transcription	GM12878-XiMat	blood
40	chr14:71228000-71245600	Weak transcription	Gastric	stomach
41	chr14:71228000-71258000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr14:71228000-71258000	Weak transcription	A549	lung
43	chr14:71228200-71251400	Weak transcription	Fetal Brain Female	brain
44	chr14:71228200-71258000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr14:71230200-71234000	Weak transcription	NHEK	skin
46	chr14:71230200-71235400	Weak transcription	HMEC	breast
47	chr14:71230400-71235400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr14:71230600-71235200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr14:71233600-71234000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr14:71233600-71238200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links