Variant report

Variant	rs354303
Chromosome Location	chr5:14255567-14255568
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14143210..14148732-chr5:14254944..14261067,10	MCF-7	breast:
2	chr5:14247745..14252723-chr5:14254933..14257114,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12522960	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154150	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs164859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs164860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs164862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs165092	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs165094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs165095	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs165096	0.94[ASN][1000 genomes]
rs16903338	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2440982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247142	0.80[JPT][hapmap]
rs30603	0.81[ASN][1000 genomes]
rs30604	0.81[ASN][1000 genomes]
rs30605	0.84[ASN][1000 genomes]
rs30618	0.82[CHB][hapmap]
rs30621	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs30623	0.80[JPT][hapmap]
rs30624	0.80[JPT][hapmap]
rs30626	0.84[ASN][1000 genomes]
rs30627	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30628	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30629	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs30630	0.85[ASN][1000 genomes]
rs30631	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs30632	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs30633	0.82[CHB][hapmap]
rs356026	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356027	0.85[ASN][1000 genomes]
rs356028	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs356029	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42253	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4701604	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56334634	0.96[ASN][1000 genomes]
rs58221971	0.93[ASN][1000 genomes]
rs6554849	0.93[ASN][1000 genomes]
rs6554850	0.96[ASN][1000 genomes]
rs6554851	0.96[ASN][1000 genomes]
rs67084079	0.83[ASN][1000 genomes]
rs72744279	0.83[ASN][1000 genomes]
rs7380307	0.82[CHB][hapmap]
rs7700787	0.82[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14247200-14256800	Weak transcription	Stomach Mucosa	stomach
2	chr5:14247400-14257000	Weak transcription	Gastric	stomach
3	chr5:14249600-14256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:14250800-14256200	Weak transcription	Small Intestine	intestine
5	chr5:14250800-14256400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:14250800-14256800	Weak transcription	Ovary	ovary
7	chr5:14250800-14257000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:14251200-14256200	Weak transcription	HepG2	liver
9	chr5:14251400-14257200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:14251800-14256400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:14251800-14257200	Weak transcription	Brain Angular Gyrus	brain
12	chr5:14252000-14256000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:14252000-14256400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:14252000-14256400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:14252000-14256800	Weak transcription	Fetal Stomach	stomach
16	chr5:14252000-14258200	Weak transcription	Brain Hippocampus Middle	brain
17	chr5:14252200-14256800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:14252200-14257000	Weak transcription	Brain Germinal Matrix	brain
19	chr5:14252200-14257000	Weak transcription	Fetal Brain Female	brain
20	chr5:14252200-14257400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:14252400-14256200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:14252400-14256800	Weak transcription	Fetal Brain Male	brain
23	chr5:14252400-14257600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:14252600-14256400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:14252600-14256600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:14252600-14257200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:14252600-14257600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr5:14252600-14259000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:14252800-14256400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:14252800-14257600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:14253000-14257000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr5:14253000-14257000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:14253000-14257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:14253000-14257600	ZNF genes & repeats	GM12878-XiMat	blood
35	chr5:14253000-14258200	Weak transcription	Pancreas	Pancrea
36	chr5:14253000-14258400	Weak transcription	Brain Substantia Nigra	brain
37	chr5:14253200-14256200	Weak transcription	Aorta	Aorta
38	chr5:14253200-14256800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:14253200-14257000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:14253200-14257000	Weak transcription	Brain Anterior Caudate	brain
41	chr5:14253200-14257000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr5:14253800-14256200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:14253800-14256200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr5:14253800-14257200	Weak transcription	Fetal Muscle Trunk	muscle
45	chr5:14253800-14257400	ZNF genes & repeats	HSMM	muscle
46	chr5:14253800-14264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr5:14254000-14256200	Weak transcription	Fetal Thymus	thymus
48	chr5:14254000-14261400	Weak transcription	Thymus	Thymus
49	chr5:14254600-14255600	Enhancers	Fetal Heart	heart
50	chr5:14254600-14255600	Enhancers	HSMMtube	muscle

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