Variant report

Variant	rs247139
Chromosome Location	chr5:14342592-14342593
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14342477..14345158-chr5:14346178..14348281,2	MCF-7	breast:
2	chr5:14340281..14342656-chr5:14350736..14353309,2	MCF-7	breast:
3	chr5:14143270..14145160-chr5:14339683..14342800,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs154152	0.86[EUR][1000 genomes]
rs154153	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154154	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154155	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154159	0.96[ASN][1000 genomes]
rs154161	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs165083	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1664507	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247134	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs247140	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247142	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs247143	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs247144	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256416	0.81[ASN][1000 genomes]
rs256417	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs256423	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30769	0.86[EUR][1000 genomes]
rs30770	0.86[EUR][1000 genomes]
rs30771	0.86[EUR][1000 genomes]
rs30782	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30783	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30784	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30792	0.85[EUR][1000 genomes]
rs39857	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs39866	0.93[ASN][1000 genomes]
rs409214	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs415341	0.85[EUR][1000 genomes]
rs42204	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs42259	0.85[EUR][1000 genomes]
rs42405	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs42407	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs42551	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14310600-14344600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:14319200-14349400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:14326800-14346400	Weak transcription	Fetal Kidney	kidney
4	chr5:14328000-14344400	Strong transcription	HMEC	breast
5	chr5:14330600-14344600	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr5:14330600-14345000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr5:14330800-14343400	Strong transcription	Fetal Muscle Leg	muscle
8	chr5:14331000-14348000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:14331400-14350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:14332600-14344400	Strong transcription	NHEK	skin
11	chr5:14333000-14343400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:14334000-14349400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:14334800-14343400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:14335000-14360600	Weak transcription	Psoas Muscle	Psoas
15	chr5:14335200-14348600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:14336400-14349400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:14337800-14346600	Weak transcription	Fetal Heart	heart
18	chr5:14338000-14357200	Weak transcription	Colonic Mucosa	Colon
19	chr5:14338200-14343400	Weak transcription	Hela-S3	cervix
20	chr5:14338400-14358000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:14338600-14348000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr5:14338800-14343000	Genic enhancers	NHLF	lung
23	chr5:14338800-14347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:14338800-14357600	Weak transcription	Esophagus	oesophagus
25	chr5:14339000-14343800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:14339000-14346400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:14339200-14342800	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr5:14339200-14344000	Weak transcription	Fetal Lung	lung
29	chr5:14339200-14357600	Weak transcription	Gastric	stomach
30	chr5:14339200-14358000	Weak transcription	Thymus	Thymus
31	chr5:14339200-14358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:14339400-14358400	Weak transcription	Fetal Thymus	thymus
33	chr5:14339600-14342600	Enhancers	Pancreas	Pancrea
34	chr5:14339600-14342800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:14339800-14348800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr5:14340000-14343000	Weak transcription	HepG2	liver
37	chr5:14340000-14347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:14340400-14353800	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr5:14340600-14342800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr5:14340600-14342800	Enhancers	Fetal Brain Female	brain
41	chr5:14340600-14343400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr5:14340600-14343400	Enhancers	H9 Cell Line	embryonic stem cell
43	chr5:14340600-14343600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr5:14340600-14344000	Enhancers	Liver	Liver
45	chr5:14340800-14342800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr5:14340800-14342800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:14340800-14342800	Enhancers	Brain Germinal Matrix	brain
48	chr5:14340800-14342800	Genic enhancers	NH-A	brain
49	chr5:14340800-14343000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:14340800-14343000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links