Variant report

Variant	rs354305
Chromosome Location	chr5:14253263-14253264
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	chr5:14141623..14144642-chr5:14252312..14255113,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11747048	1.00[CHB][hapmap]
rs13175673	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13184211	1.00[CHB][hapmap]
rs13184670	1.00[CHB][hapmap]
rs164861	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299045	1.00[CHB][hapmap]
rs17302408	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs187125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2434605	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs245577	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591277	0.99[EUR][1000 genomes]
rs26057	1.00[CHB][hapmap]
rs26058	1.00[CHB][hapmap]
rs26059	1.00[CHB][hapmap]
rs26061	1.00[CHB][hapmap]
rs2607077	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607078	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697663	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27665	1.00[CHB][hapmap]
rs28010	1.00[CHB][hapmap]
rs30616	1.00[CHB][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs30617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32339	1.00[CHB][hapmap]
rs32341	1.00[CHB][hapmap]
rs32390	1.00[CHB][hapmap]
rs32394	1.00[CHB][hapmap]
rs354285	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs354298	1.00[CHB][hapmap]
rs354300	1.00[CHB][hapmap]
rs354308	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs354312	1.00[CHB][hapmap]
rs3849082	1.00[CHB][hapmap]
rs39856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42485	1.00[ASN][1000 genomes]
rs4702028	1.00[CHB][hapmap]
rs706271	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773701	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773703	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs773763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.96[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799025	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897724	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897726	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923616	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14247200-14256800	Weak transcription	Stomach Mucosa	stomach
2	chr5:14247400-14254600	Weak transcription	Hela-S3	cervix
3	chr5:14247400-14257000	Weak transcription	Gastric	stomach
4	chr5:14248400-14253800	Enhancers	Fetal Muscle Trunk	muscle
5	chr5:14248400-14255400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:14248600-14255000	Enhancers	Psoas Muscle	Psoas
7	chr5:14248800-14253800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:14248800-14254000	Enhancers	Fetal Thymus	thymus
9	chr5:14249400-14254800	Enhancers	Lung	lung
10	chr5:14249600-14256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:14250000-14254000	Enhancers	Thymus	Thymus
12	chr5:14250600-14255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:14250800-14253800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:14250800-14253800	Weak transcription	K562	blood
15	chr5:14250800-14255200	Weak transcription	NHDF-Ad	bronchial
16	chr5:14250800-14256200	Weak transcription	Small Intestine	intestine
17	chr5:14250800-14256400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:14250800-14256800	Weak transcription	Ovary	ovary
19	chr5:14250800-14257000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:14251200-14256200	Weak transcription	HepG2	liver
21	chr5:14251400-14253800	Weak transcription	HUVEC	blood vessel
22	chr5:14251400-14254200	Weak transcription	Fetal Intestine Small	intestine
23	chr5:14251400-14255000	Enhancers	Left Ventricle	heart
24	chr5:14251400-14255200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:14251400-14257200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:14251600-14255200	Weak transcription	Osteobl	bone
27	chr5:14251800-14253800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:14251800-14254600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:14251800-14254600	Weak transcription	Spleen	Spleen
30	chr5:14251800-14254600	Weak transcription	HSMMtube	muscle
31	chr5:14251800-14254600	Weak transcription	NH-A	brain
32	chr5:14251800-14255200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:14251800-14256400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:14251800-14257200	Weak transcription	Brain Angular Gyrus	brain
35	chr5:14252000-14255200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr5:14252000-14255200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr5:14252000-14256000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:14252000-14256400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:14252000-14256400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr5:14252000-14256800	Weak transcription	Fetal Stomach	stomach
41	chr5:14252000-14258200	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:14252200-14254200	Enhancers	Fetal Heart	heart
43	chr5:14252200-14254800	Enhancers	Right Ventricle	heart
44	chr5:14252200-14255400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr5:14252200-14256800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:14252200-14257000	Weak transcription	Brain Germinal Matrix	brain
47	chr5:14252200-14257000	Weak transcription	Fetal Brain Female	brain
48	chr5:14252200-14257400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:14252400-14254000	ZNF genes & repeats	NHEK	skin
50	chr5:14252400-14254800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin

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