Variant report

Variant	rs4420472
Chromosome Location	chr15:59539794-59539795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59538258..59540187-chr15:59575748..59578001,2	MCF-7	breast:
2	chr15:59539485..59542336-chr15:59663424..59665650,3	MCF-7	breast:
3	chr15:59539475..59539997-chr15:59704300..59705075,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157470	Chromatin interaction
ENSG00000157483	Chromatin interaction

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

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

rs_ID	r²[population]
rs10775169	0.84[EUR][1000 genomes]
rs11855088	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12437559	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12437571	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439560	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12441621	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12443328	0.94[CEU][hapmap]
rs12593382	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12595001	0.84[CEU][hapmap]
rs12595677	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12912088	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917076	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17236495	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17236502	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17236509	0.89[CEU][hapmap]
rs17302240	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17302247	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2306783	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2306784	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2414624	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28368974	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34310505	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34540528	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34827755	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3794489	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4074433	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4074434	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4077169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4287498	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4482215	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4597251	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4775137	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56752228	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6494081	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6494091	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67037466	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67599725	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs68078916	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs68084852	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166002	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7180541	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72625730	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72746841	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8030006	0.89[AMR][1000 genomes]
rs8031729	0.89[CEU][hapmap]
rs8039095	0.89[CEU][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv904272	chr15:59500577-59549018	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv904273	chr15:59518488-59567137	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59511400-59549200	Weak transcription	Colonic Mucosa	Colon
2	chr15:59515800-59566600	Weak transcription	Pancreas	Pancrea
3	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
6	chr15:59524000-59541800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:59524000-59542200	Weak transcription	Gastric	stomach
8	chr15:59524000-59546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:59524600-59574600	Weak transcription	Lung	lung
11	chr15:59524800-59542200	Weak transcription	Esophagus	oesophagus
12	chr15:59525000-59541800	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:59525000-59546400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:59525200-59540200	Weak transcription	Right Ventricle	heart
15	chr15:59525200-59543000	Weak transcription	Right Atrium	heart
16	chr15:59525200-59547800	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:59525200-59554000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
19	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:59525400-59541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:59525400-59542200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:59529200-59540800	Weak transcription	Adipose Nuclei	Adipose
23	chr15:59529200-59547200	Weak transcription	Aorta	Aorta
24	chr15:59529200-59547800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:59529800-59539800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:59529800-59545000	Weak transcription	HepG2	liver
27	chr15:59530200-59548000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:59530400-59539800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:59530600-59539800	Weak transcription	Left Ventricle	heart
30	chr15:59530600-59539800	Weak transcription	HUVEC	blood vessel
31	chr15:59530600-59558200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:59530600-59568000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:59530800-59543200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr15:59530800-59549400	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr15:59530800-59569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:59532800-59544200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:59533200-59539800	Weak transcription	Fetal Kidney	kidney
38	chr15:59533400-59541000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:59533400-59541800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:59533400-59542000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:59533400-59543200	Weak transcription	NHDF-Ad	bronchial
42	chr15:59533400-59559800	Weak transcription	NHLF	lung
43	chr15:59533400-59564000	Weak transcription	Ovary	ovary
44	chr15:59533400-59566800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:59534400-59539800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:59534400-59540000	Strong transcription	Osteobl	bone
47	chr15:59534400-59542200	Weak transcription	Fetal Stomach	stomach
48	chr15:59534400-59547800	Genic enhancers	A549	lung
49	chr15:59535200-59542000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:59535200-59542000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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