Variant report

Variant	rs12899638
Chromosome Location	chr15:58920275-58920276
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58919916..58921624-chr15:58929696..58932530,2	K562	blood:
2	chr15:58915714..58920888-chr15:58922126..58927407,8	K562	blood:
3	chr15:58915714..58921238-chr15:58922986..58925558,6	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11071398	0.95[YRI][hapmap]
rs11638244	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11854073	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12439457	0.84[AFR][1000 genomes]
rs12594872	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12900643	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12912699	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1427282	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1469343	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1648532	0.88[YRI][hapmap]
rs2555356	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs2657125	1.00[YRI][hapmap]
rs28864995	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs347115	0.95[YRI][hapmap]
rs347117	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs383902	0.95[YRI][hapmap]
rs387812	0.88[CHB][hapmap];0.95[YRI][hapmap]
rs395601	0.88[CHB][hapmap]
rs411007	0.88[CHB][hapmap]
rs4275799	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs442495	1.00[YRI][hapmap]
rs474875	0.95[YRI][hapmap]
rs4775083	0.89[ASN][1000 genomes]
rs4775087	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs514049	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs610877	0.95[YRI][hapmap]
rs6494026	0.85[ASN][1000 genomes]
rs6494029	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]
rs714696	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7161889	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7163162	0.84[AFR][1000 genomes]
rs7166356	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7168776	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7171098	0.85[ASN][1000 genomes]
rs8035373	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8043406	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs972801	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:58889800-58921000	Weak transcription	Ovary	ovary
3	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:58905000-58920800	Weak transcription	Left Ventricle	heart
5	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
6	chr15:58905400-58971800	Weak transcription	Spleen	Spleen
7	chr15:58905600-58976400	Weak transcription	Gastric	stomach
8	chr15:58906400-58923000	Weak transcription	Pancreas	Pancrea
9	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
10	chr15:58907200-58920600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:58907200-58920800	Weak transcription	NH-A	brain
12	chr15:58907400-58920800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:58907800-58952000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:58908000-58923000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:58909000-58920800	Weak transcription	Hela-S3	cervix
16	chr15:58910400-58923200	Weak transcription	Lung	lung
17	chr15:58910400-58934000	Weak transcription	Psoas Muscle	Psoas
18	chr15:58910800-58926200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:58911600-58951200	Weak transcription	Fetal Brain Male	brain
20	chr15:58911600-58958000	Weak transcription	Fetal Brain Female	brain
21	chr15:58912600-58920800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:58912600-58922800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:58914200-58957600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:58914600-58957000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:58915600-58920800	Weak transcription	Right Ventricle	heart
26	chr15:58915800-58920600	Weak transcription	HSMMtube	muscle
27	chr15:58916800-58920400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:58916800-58920400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:58917000-58923000	Weak transcription	Fetal Stomach	stomach
30	chr15:58917000-58959600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:58917600-58925600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:58918400-58920600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:58918600-58920800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:58918800-58920600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr15:58919000-58920400	Strong transcription	NHEK	skin
36	chr15:58919000-58923000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:58919400-58920800	Enhancers	Brain Cingulate Gyrus	brain
38	chr15:58919400-58920800	Enhancers	Brain Hippocampus Middle	brain
39	chr15:58919400-58921200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:58919600-58920600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:58919600-58920600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:58919600-58920600	Enhancers	Adipose Nuclei	Adipose
43	chr15:58919600-58920600	Enhancers	Liver	Liver
44	chr15:58919600-58920800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:58919600-58920800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:58919600-58920800	Enhancers	Brain Anterior Caudate	brain
47	chr15:58919600-58920800	Weak transcription	Fetal Muscle Leg	muscle
48	chr15:58919600-58920800	Genic enhancers	HSMM	muscle
49	chr15:58919600-58921200	Active TSS	Thymus	Thymus
50	chr15:58919600-58921600	Flanking Active TSS	Primary T cells from cord blood	blood

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