Variant report

Variant	rs247140
Chromosome Location	chr5:14344689-14344690
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	chr5:14342477..14345158-chr5:14346178..14348281,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs154150	0.81[CEU][hapmap]
rs154152	0.86[EUR][1000 genomes]
rs154153	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154154	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154155	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs154159	0.93[ASN][1000 genomes]
rs154161	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs165083	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1664507	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16903338	0.81[CEU][hapmap]
rs247134	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs247139	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247141	0.88[JPT][hapmap]
rs247142	1.00[CEU][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs247143	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs247144	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs256417	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs256423	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30623	0.87[JPT][hapmap]
rs30624	0.87[JPT][hapmap]
rs30769	0.86[EUR][1000 genomes]
rs30770	0.86[EUR][1000 genomes]
rs30771	0.86[EUR][1000 genomes]
rs30782	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30783	0.94[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30784	0.93[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30792	0.81[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs39857	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs39866	0.90[ASN][1000 genomes]
rs409214	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs415341	0.85[EUR][1000 genomes]
rs42204	0.82[AMR][1000 genomes]
rs42259	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs42405	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs42407	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs42551	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14319200-14349400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:14326800-14346400	Weak transcription	Fetal Kidney	kidney
3	chr5:14330600-14345000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr5:14331000-14348000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:14331400-14350000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:14334000-14349400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:14335000-14360600	Weak transcription	Psoas Muscle	Psoas
8	chr5:14335200-14348600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:14336400-14349400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:14337800-14346600	Weak transcription	Fetal Heart	heart
11	chr5:14338000-14357200	Weak transcription	Colonic Mucosa	Colon
12	chr5:14338400-14358000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:14338600-14348000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:14338800-14347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:14338800-14357600	Weak transcription	Esophagus	oesophagus
16	chr5:14339000-14346400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:14339200-14357600	Weak transcription	Gastric	stomach
18	chr5:14339200-14358000	Weak transcription	Thymus	Thymus
19	chr5:14339200-14358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:14339400-14358400	Weak transcription	Fetal Thymus	thymus
21	chr5:14339800-14348800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:14340000-14347000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:14340400-14353800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr5:14340800-14353600	Strong transcription	HSMM	muscle
25	chr5:14341200-14350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:14341400-14355000	Weak transcription	Ovary	ovary
27	chr5:14341400-14359400	Weak transcription	Primary T cells from cord blood	blood
28	chr5:14341600-14347400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:14341600-14348600	Weak transcription	Aorta	Aorta
30	chr5:14341600-14357400	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:14342400-14347600	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:14342600-14346200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:14342600-14346400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:14342600-14346400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr5:14342600-14357200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:14342600-14358200	Weak transcription	Pancreas	Pancrea
37	chr5:14342800-14345400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:14342800-14346200	Weak transcription	Fetal Stomach	stomach
39	chr5:14342800-14346600	Weak transcription	Fetal Intestine Small	intestine
40	chr5:14342800-14347600	Weak transcription	Stomach Mucosa	stomach
41	chr5:14342800-14348400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr5:14342800-14348600	Weak transcription	Spleen	Spleen
43	chr5:14342800-14350000	Weak transcription	Brain Germinal Matrix	brain
44	chr5:14342800-14351000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr5:14342800-14351600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:14342800-14352000	Strong transcription	Osteobl	bone
47	chr5:14342800-14352200	Strong transcription	NH-A	brain
48	chr5:14342800-14354000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr5:14342800-14355000	Weak transcription	Right Ventricle	heart
50	chr5:14342800-14357200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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