Variant report

Variant	rs2898974
Chromosome Location	chr15:40305162-40305163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11070241	0.88[JPT][hapmap]
rs11633992	0.93[EUR][1000 genomes]
rs12050693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12050884	1.00[CEU][hapmap];0.97[ASN][1000 genomes]
rs12591670	1.00[CEU][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes]
rs12901892	1.00[CEU][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1436278	0.81[JPT][hapmap]
rs1689605	0.81[JPT][hapmap]
rs16970030	0.82[JPT][hapmap]
rs16970033	0.82[JPT][hapmap]
rs16970098	0.80[JPT][hapmap]
rs16970132	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs16970168	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16970181	0.84[YRI][hapmap]
rs16970197	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16970202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2196470	0.82[JPT][hapmap]
rs2279580	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2291623	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412460	0.83[ASN][1000 genomes]
rs2412473	0.90[MEX][hapmap]
rs2898985	0.85[MEX][hapmap]
rs35390951	0.82[JPT][hapmap]
rs4432245	0.85[MEX][hapmap]
rs4566130	0.82[JPT][hapmap]
rs4594236	0.84[MEX][hapmap]
rs4924407	0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4924408	0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs503671	0.82[JPT][hapmap]
rs58367544	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs711906	0.85[MEX][hapmap]
rs7165105	0.82[JPT][hapmap]
rs7178419	0.88[JPT][hapmap]
rs73390620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:40277800-40305400	Strong transcription	Fetal Muscle Leg	muscle
3	chr15:40277800-40305600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:40278000-40305400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:40291600-40305800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:40291800-40305200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:40291800-40305800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:40292000-40306600	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:40292400-40305800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:40292600-40306400	Strong transcription	Primary T cells from cord blood	blood
11	chr15:40292800-40306400	Strong transcription	Adipose Nuclei	Adipose
12	chr15:40293000-40306600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr15:40293000-40306800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr15:40293000-40315000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr15:40293200-40305400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:40293200-40306000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr15:40293200-40306200	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr15:40293400-40305600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:40294400-40305800	Strong transcription	Fetal Thymus	thymus
20	chr15:40294400-40306400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:40295000-40305400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:40295000-40306200	Strong transcription	NHEK	skin
23	chr15:40296000-40311400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:40296200-40306200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr15:40296200-40313000	Weak transcription	Psoas Muscle	Psoas
26	chr15:40296400-40306400	Weak transcription	Stomach Mucosa	stomach
27	chr15:40296400-40313200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:40296400-40325200	Weak transcription	Hela-S3	cervix
29	chr15:40298400-40306200	Strong transcription	Placenta	Placenta
30	chr15:40298800-40306200	Strong transcription	HepG2	liver
31	chr15:40298800-40306400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:40299000-40306600	Strong transcription	Fetal Lung	lung
33	chr15:40299000-40306600	Strong transcription	Left Ventricle	heart
34	chr15:40299000-40307000	Strong transcription	NHLF	lung
35	chr15:40299000-40308400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:40299200-40306200	Strong transcription	Fetal Intestine Large	intestine
37	chr15:40299400-40306600	Strong transcription	Rectal Smooth Muscle	rectum
38	chr15:40299600-40306000	Strong transcription	Fetal Stomach	stomach
39	chr15:40299600-40306200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:40299600-40307000	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:40300200-40305600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr15:40300200-40306400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:40301000-40305600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:40301000-40305600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:40301000-40305800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:40301000-40306600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:40301000-40311600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr15:40301000-40322000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:40301200-40306200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:40301200-40313000	Weak transcription	K562	blood

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