Variant report

Variant	rs6494084
Chromosome Location	chr15:59534717-59534718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs3794488	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57487429	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58579379	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59773793	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62002697	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494079	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494086	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6494087	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494089	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172489	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172761	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7174147	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7175876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7179352	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181249	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027055	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8027766	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8038705	0.92[EUR][1000 genomes]
rs8040147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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:81 , 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	chr15:59517000-59536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:59517600-59546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:59517800-59564200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
7	chr15:59524000-59541800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr15:59524000-59542200	Weak transcription	Gastric	stomach
9	chr15:59524000-59546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:59524600-59574600	Weak transcription	Lung	lung
12	chr15:59524800-59542200	Weak transcription	Esophagus	oesophagus
13	chr15:59525000-59541800	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:59525000-59546400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:59525200-59540200	Weak transcription	Right Ventricle	heart
16	chr15:59525200-59543000	Weak transcription	Right Atrium	heart
17	chr15:59525200-59547800	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:59525200-59554000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
20	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:59525400-59534800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:59525400-59541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:59525400-59542200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:59527400-59536000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:59529200-59535600	Weak transcription	Stomach Mucosa	stomach
26	chr15:59529200-59540800	Weak transcription	Adipose Nuclei	Adipose
27	chr15:59529200-59547200	Weak transcription	Aorta	Aorta
28	chr15:59529200-59547800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr15:59529600-59535600	Weak transcription	NH-A	brain
30	chr15:59529800-59539800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:59529800-59545000	Weak transcription	HepG2	liver
32	chr15:59530200-59548000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:59530400-59538600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:59530400-59539600	Weak transcription	Primary B cells from cord blood	blood
35	chr15:59530400-59539800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:59530600-59536400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:59530600-59539800	Weak transcription	Left Ventricle	heart
38	chr15:59530600-59539800	Weak transcription	HUVEC	blood vessel
39	chr15:59530600-59558200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:59530600-59568000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:59530800-59543200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr15:59530800-59549400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr15:59530800-59569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:59531000-59535600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:59531800-59536000	Strong transcription	Hela-S3	cervix
46	chr15:59532000-59536600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:59532000-59539200	Strong transcription	HMEC	breast
48	chr15:59532400-59539600	Strong transcription	NHEK	skin
49	chr15:59532600-59536200	Strong transcription	GM12878-XiMat	blood
50	chr15:59532800-59536800	Strong transcription	Fetal Intestine Small	intestine

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