Variant report

Variant	rs2028546
Chromosome Location	chr15:78321812-78321813
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1004855	0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10519181	0.86[CHB][hapmap]
rs11072716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11631578	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11634607	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11638311	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852768	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12148365	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12442213	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12591418	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12594823	0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12901812	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12907701	0.81[ASN][1000 genomes]
rs12907814	0.82[ASN][1000 genomes]
rs12911332	0.85[CHB][hapmap];0.84[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12916362	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1348257	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1442293	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1837913	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2044099	0.91[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2241885	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867985	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2903702	0.82[ASN][1000 genomes]
rs3803380	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4395040	0.86[CHB][hapmap]
rs4886553	0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4886554	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4886994	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4886996	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4886999	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4887000	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55704745	0.94[ASN][1000 genomes]
rs57220134	0.81[ASN][1000 genomes]
rs58578288	0.81[ASN][1000 genomes]
rs62011511	0.81[ASN][1000 genomes]
rs7166819	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7170746	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7173128	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174489	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7181594	0.83[ASN][1000 genomes]
rs8030713	0.86[ASN][1000 genomes]
rs8030873	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	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	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78301400-78342200	Weak transcription	HMEC	breast
3	chr15:78303200-78342400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:78305400-78329800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:78305600-78325800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:78307200-78342000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:78308800-78327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:78309200-78330200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:78309200-78330800	Weak transcription	A549	lung
10	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:78311200-78322600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:78311800-78322400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr15:78311800-78323400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:78311800-78326800	Weak transcription	K562	blood
15	chr15:78312000-78323000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:78312200-78322800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:78312200-78323200	Strong transcription	Fetal Intestine Large	intestine
18	chr15:78312400-78322200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:78312400-78322400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr15:78312400-78322400	Strong transcription	Thymus	Thymus
21	chr15:78312400-78322600	Strong transcription	Primary T cells from cord blood	blood
22	chr15:78312400-78323200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:78312600-78322400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:78312600-78322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:78312600-78322600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:78312600-78322800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:78312600-78323200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:78312600-78323400	Strong transcription	Dnd41	blood
29	chr15:78312600-78323400	Strong transcription	Osteobl	bone
30	chr15:78312800-78322600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:78312800-78323200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:78313000-78327600	Weak transcription	Fetal Brain Male	brain
33	chr15:78316000-78324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr15:78316000-78332400	Weak transcription	Hela-S3	cervix
35	chr15:78316200-78323200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr15:78316200-78324600	Strong transcription	Fetal Intestine Small	intestine
37	chr15:78316200-78326200	Weak transcription	Fetal Kidney	kidney
38	chr15:78317000-78324200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:78317000-78327800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:78317200-78324000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr15:78317400-78323200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr15:78317400-78324200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:78317400-78326000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:78317400-78326200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:78317400-78342600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:78317600-78324600	Strong transcription	Liver	Liver
48	chr15:78317600-78326800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:78317600-78327000	Weak transcription	NH-A	brain
50	chr15:78317600-78327400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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