Variant report

Variant	rs17302240
Chromosome Location	chr15:59534293-59534294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10775169	0.90[EUR][1000 genomes]
rs11855088	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12437571	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441621	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12443328	0.94[CEU][hapmap]
rs12593382	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12595001	0.84[CEU][hapmap]
rs12595677	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912088	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12917076	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17236495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236502	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17236509	0.89[CEU][hapmap]
rs17302247	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306783	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306784	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414624	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28368974	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34310505	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34540528	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34827755	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794489	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4074433	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4074434	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077169	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4287498	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4420472	1.00[CEU][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4482215	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4597251	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4775137	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56752228	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6494091	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67037466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67599725	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68078916	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68084852	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7166002	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180541	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72625730	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72746841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030006	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][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:80 , 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	chr15:59521600-59534400	Weak transcription	Placenta	Placenta
7	chr15:59521600-59566400	Weak transcription	Psoas Muscle	Psoas
8	chr15:59524000-59541800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:59524000-59542200	Weak transcription	Gastric	stomach
10	chr15:59524000-59546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:59524600-59569200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:59524600-59574600	Weak transcription	Lung	lung
13	chr15:59524800-59542200	Weak transcription	Esophagus	oesophagus
14	chr15:59525000-59541800	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:59525000-59546400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:59525200-59540200	Weak transcription	Right Ventricle	heart
17	chr15:59525200-59543000	Weak transcription	Right Atrium	heart
18	chr15:59525200-59547800	Weak transcription	Colon Smooth Muscle	Colon
19	chr15:59525200-59554000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:59525200-59566600	Weak transcription	Small Intestine	intestine
21	chr15:59525200-59582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:59525400-59534800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:59525400-59541000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:59525400-59542200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:59527400-59534600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:59527400-59536000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:59529200-59535600	Weak transcription	Stomach Mucosa	stomach
28	chr15:59529200-59540800	Weak transcription	Adipose Nuclei	Adipose
29	chr15:59529200-59547200	Weak transcription	Aorta	Aorta
30	chr15:59529200-59547800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr15:59529600-59535600	Weak transcription	NH-A	brain
32	chr15:59529800-59539800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:59529800-59545000	Weak transcription	HepG2	liver
34	chr15:59530000-59534400	Weak transcription	Liver	Liver
35	chr15:59530200-59548000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:59530400-59538600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:59530400-59539600	Weak transcription	Primary B cells from cord blood	blood
38	chr15:59530400-59539800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:59530600-59534600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr15:59530600-59536400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:59530600-59539800	Weak transcription	Left Ventricle	heart
42	chr15:59530600-59539800	Weak transcription	HUVEC	blood vessel
43	chr15:59530600-59558200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:59530600-59568000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:59530800-59534400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:59530800-59543200	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:59530800-59549400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:59530800-59569000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:59531000-59535600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:59531800-59536000	Strong transcription	Hela-S3	cervix

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