Variant report

Variant	rs30603
Chromosome Location	chr5:14257829-14257830
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14142719..14145389-chr5:14255713..14258192,4	MCF-7	breast:
2	chr5:14152848..14154362-chr5:14257510..14259958,2	MCF-7	breast:
3	chr5:14143210..14148732-chr5:14254944..14261067,10	MCF-7	breast:
4	chr5:14257321..14259050-chr5:14260298..14262168,2	K562	blood:
5	chr5:14246723..14248369-chr5:14255798..14258024,2	MCF-7	breast:
6	chr5:14255845..14258384-chr5:14262309..14265414,3	MCF-7	breast:
7	chr5:14035881..14037914-chr5:14255980..14258485,2	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	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154150	0.82[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	0.95[EUR][1000 genomes]
rs16903338	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30604	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30605	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30618	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	0.95[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	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72744279	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7380307	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7700787	0.82[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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14252000-14258200	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:14252600-14259000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:14253000-14258200	Weak transcription	Pancreas	Pancrea
4	chr5:14253000-14258400	Weak transcription	Brain Substantia Nigra	brain
5	chr5:14253800-14264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:14254000-14261400	Weak transcription	Thymus	Thymus
7	chr5:14254600-14258200	ZNF genes & repeats	A549	lung
8	chr5:14255400-14260400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr5:14255400-14262400	Enhancers	HUVEC	blood vessel
10	chr5:14255600-14258200	Weak transcription	Psoas Muscle	Psoas
11	chr5:14255600-14258400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:14255600-14259800	Enhancers	Left Ventricle	heart
13	chr5:14256000-14258400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:14256000-14259400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:14256200-14258200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr5:14256200-14258600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr5:14256200-14258800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:14256200-14260400	Enhancers	Fetal Thymus	thymus
19	chr5:14256200-14264200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr5:14256400-14258000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:14256400-14258800	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr5:14256400-14258800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:14256400-14258800	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr5:14256400-14259000	Enhancers	H9 Cell Line	embryonic stem cell
25	chr5:14256400-14259200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:14256400-14259200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:14256400-14259200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr5:14256400-14259200	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr5:14256400-14265400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:14256600-14258200	Weak transcription	Esophagus	oesophagus
31	chr5:14256600-14258600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:14256600-14258800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:14256600-14259800	Enhancers	Adipose Nuclei	Adipose
34	chr5:14256600-14264400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:14256800-14258800	Enhancers	Ovary	ovary
36	chr5:14256800-14259000	Enhancers	Fetal Brain Male	brain
37	chr5:14256800-14259200	Enhancers	Colonic Mucosa	Colon
38	chr5:14256800-14259200	Enhancers	Fetal Muscle Leg	muscle
39	chr5:14256800-14259200	Enhancers	Right Atrium	heart
40	chr5:14256800-14259200	Enhancers	Right Ventricle	heart
41	chr5:14256800-14260200	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr5:14256800-14261800	Enhancers	Colon Smooth Muscle	Colon
43	chr5:14257000-14258000	Weak transcription	Fetal Intestine Small	intestine
44	chr5:14257000-14258400	Genic enhancers	Osteobl	bone
45	chr5:14257000-14258800	Enhancers	Rectal Smooth Muscle	rectum
46	chr5:14257000-14258800	Weak transcription	NHDF-Ad	bronchial
47	chr5:14257000-14259200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:14257000-14259200	Enhancers	Gastric	stomach
49	chr5:14257000-14259200	Enhancers	Spleen	Spleen
50	chr5:14257000-14259400	Enhancers	Skeletal Muscle Male	skeletal muscle

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