Variant report

Variant	rs6494029
Chromosome Location	chr15:58923206-58923207
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58915714..58920888-chr15:58922126..58927407,8	K562	blood:
2	chr15:58915714..58921238-chr15:58922986..58925558,6	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11071398	0.95[YRI][hapmap]
rs11638244	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11854073	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12439457	0.86[AFR][1000 genomes]
rs12594872	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899638	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900643	0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12912699	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1427282	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1469343	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1648532	0.86[YRI][hapmap]
rs2555356	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs2657125	1.00[YRI][hapmap]
rs28864995	1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs347115	1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs347117	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs383902	1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs387812	1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs395601	1.00[CHB][hapmap]
rs411007	1.00[CHB][hapmap]
rs4275799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs442495	1.00[YRI][hapmap]
rs474875	1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs4775083	0.85[ASN][1000 genomes]
rs4775086	0.82[MKK][hapmap]
rs4775087	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs514049	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs605928	0.80[MKK][hapmap]
rs610877	1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs6494026	0.81[ASN][1000 genomes]
rs682619	0.86[CHB][hapmap]
rs714696	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7161889	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7163162	0.86[AFR][1000 genomes]
rs7166356	1.00[CHB][hapmap]
rs7168776	1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7171098	0.81[ASN][1000 genomes]
rs8035373	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs8043406	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs972801	0.81[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1551	chr15:58891639-58936580	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv569602	chr15:58914326-58964437	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
3	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
4	chr15:58905600-58976400	Weak transcription	Gastric	stomach
5	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
6	chr15:58907800-58952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:58910400-58934000	Weak transcription	Psoas Muscle	Psoas
8	chr15:58910800-58926200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:58911600-58951200	Weak transcription	Fetal Brain Male	brain
10	chr15:58911600-58958000	Weak transcription	Fetal Brain Female	brain
11	chr15:58914200-58957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:58914600-58957000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:58917600-58925600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:58919800-58924200	Weak transcription	Fetal Lung	lung
16	chr15:58919800-58959200	Weak transcription	Brain Germinal Matrix	brain
17	chr15:58920000-58923600	Weak transcription	K562	blood
18	chr15:58920200-58923800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:58920200-58924200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:58920200-58930000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:58920200-58946600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:58920200-58957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:58920400-58924000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:58920400-58933000	Weak transcription	Fetal Kidney	kidney
25	chr15:58921000-58929000	Weak transcription	Left Ventricle	heart
26	chr15:58921000-58957600	Weak transcription	Colonic Mucosa	Colon
27	chr15:58921200-58924400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:58921200-58930200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:58921200-58931000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr15:58921200-58932200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:58921200-58932200	Weak transcription	HSMMtube	muscle
32	chr15:58921200-58933000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:58921200-58933800	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:58921200-58946400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr15:58921200-58946600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:58921200-58946800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:58921200-58949400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:58921200-58959600	Weak transcription	Aorta	Aorta
39	chr15:58921200-58968400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr15:58921400-58926400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:58921400-58929800	Weak transcription	NH-A	brain
42	chr15:58921600-58923400	Weak transcription	Adipose Nuclei	Adipose
43	chr15:58921600-58923400	Weak transcription	Brain Substantia Nigra	brain
44	chr15:58921600-58923600	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:58921600-58923600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr15:58921600-58924000	Genic enhancers	Fetal Thymus	thymus
47	chr15:58921600-58924400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:58921600-58924600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:58921600-58924600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:58921600-58926800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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