Variant report

Variant	rs30604
Chromosome Location	chr5:14258517-14258518
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14152848..14154362-chr5:14257510..14259958,2	MCF-7	breast:
2	chr5:14143210..14148732-chr5:14254944..14261067,10	MCF-7	breast:
3	chr5:14257321..14259050-chr5:14260298..14262168,2	K562	blood:
4	chr17:63496254..63496856-chr5:14258373..14258873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12659261	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154150	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154153	0.82[EUR][1000 genomes]
rs154154	0.82[EUR][1000 genomes]
rs154155	0.82[EUR][1000 genomes]
rs164862	0.85[ASN][1000 genomes]
rs165083	0.82[EUR][1000 genomes]
rs165095	0.82[ASN][1000 genomes]
rs165096	0.82[ASN][1000 genomes]
rs16903326	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16903338	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30603	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30605	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30618	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs354303	0.81[ASN][1000 genomes]
rs42204	0.86[EUR][1000 genomes]
rs42405	0.82[EUR][1000 genomes]
rs56226439	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56334634	0.84[ASN][1000 genomes]
rs58221971	0.87[ASN][1000 genomes]
rs6554849	0.87[ASN][1000 genomes]
rs6554850	0.84[ASN][1000 genomes]
rs6554851	0.84[ASN][1000 genomes]
rs67084079	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72744279	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7380307	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7700787	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]

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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14252600-14259000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:14253800-14264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:14254000-14261400	Weak transcription	Thymus	Thymus
4	chr5:14255400-14260400	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr5:14255400-14262400	Enhancers	HUVEC	blood vessel
6	chr5:14255600-14259800	Enhancers	Left Ventricle	heart
7	chr5:14256000-14259400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:14256200-14258600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:14256200-14258800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:14256200-14260400	Enhancers	Fetal Thymus	thymus
11	chr5:14256200-14264200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:14256400-14258800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:14256400-14258800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr5:14256400-14258800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:14256400-14259000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr5:14256400-14259200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:14256400-14259200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:14256400-14259200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr5:14256400-14259200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr5:14256400-14265400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:14256600-14258600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:14256600-14258800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:14256600-14259800	Enhancers	Adipose Nuclei	Adipose
24	chr5:14256600-14264400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:14256800-14258800	Enhancers	Ovary	ovary
26	chr5:14256800-14259000	Enhancers	Fetal Brain Male	brain
27	chr5:14256800-14259200	Enhancers	Colonic Mucosa	Colon
28	chr5:14256800-14259200	Enhancers	Fetal Muscle Leg	muscle
29	chr5:14256800-14259200	Enhancers	Right Atrium	heart
30	chr5:14256800-14259200	Enhancers	Right Ventricle	heart
31	chr5:14256800-14260200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr5:14256800-14261800	Enhancers	Colon Smooth Muscle	Colon
33	chr5:14257000-14258800	Enhancers	Rectal Smooth Muscle	rectum
34	chr5:14257000-14258800	Weak transcription	NHDF-Ad	bronchial
35	chr5:14257000-14259200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:14257000-14259200	Enhancers	Gastric	stomach
37	chr5:14257000-14259200	Enhancers	Spleen	Spleen
38	chr5:14257000-14259400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr5:14257000-14260200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr5:14257000-14260200	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:14257000-14260400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr5:14257000-14260400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:14257000-14260600	Enhancers	Fetal Heart	heart
44	chr5:14257000-14264600	Enhancers	NH-A	brain
45	chr5:14257200-14258600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:14257200-14258800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:14257200-14259000	Enhancers	Stomach Smooth Muscle	stomach
48	chr5:14257200-14259200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr5:14257200-14259200	Enhancers	Duodenum Mucosa	Duodenum
50	chr5:14257200-14259200	Enhancers	Fetal Muscle Trunk	muscle

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