Variant report

Variant	rs16940998
Chromosome Location	chr15:59378294-59378295
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10431762	0.92[ASN][1000 genomes]
rs10431791	0.91[CEU][hapmap]
rs10518996	0.81[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs1074702	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10851642	0.95[ASN][1000 genomes]
rs10851643	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11071405	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11071407	0.82[EUR][1000 genomes]
rs11852461	0.95[CEU][hapmap];0.85[AMR][1000 genomes]
rs11855536	0.92[CEU][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12050865	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437587	0.82[ASN][1000 genomes]
rs12438128	0.85[ASN][1000 genomes]
rs12438208	0.86[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs12438962	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs12440692	0.91[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs12441973	0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12442086	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12442134	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12442301	0.96[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12900369	0.86[ASN][1000 genomes]
rs12902628	0.86[ASN][1000 genomes]
rs12906212	0.86[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs12907187	0.86[ASN][1000 genomes]
rs12907277	0.81[ASN][1000 genomes]
rs12907548	0.88[LWK][hapmap]
rs12907957	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910987	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12912429	0.95[ASN][1000 genomes]
rs12913177	0.81[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs12915899	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12917373	0.90[ASN][1000 genomes]
rs1345116	0.83[AMR][1000 genomes]
rs1374155	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1446237	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1446238	1.00[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1446239	0.82[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap]
rs1665049	0.80[CHD][hapmap]
rs1665050	0.83[CHD][hapmap]
rs1665051	0.82[CHD][hapmap]
rs16940987	0.81[LWK][hapmap]
rs16941014	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17236369	0.86[CEU][hapmap]
rs17236383	0.81[ASW][hapmap];0.90[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17236453	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17302142	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17302163	0.82[ASN][1000 genomes]
rs17302191	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1867757	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1968606	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1968607	0.87[ASN][1000 genomes]
rs1971181	0.94[ASN][1000 genomes]
rs1975534	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2084161	0.81[CHB][hapmap];0.85[GIH][hapmap]
rs2121236	0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2121237	0.86[ASN][1000 genomes]
rs2289895	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2414618	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28383505	0.83[ASN][1000 genomes]
rs28383522	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28391430	0.86[ASN][1000 genomes]
rs28514475	0.86[ASN][1000 genomes]
rs28610479	0.86[ASN][1000 genomes]
rs2899640	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs34338282	0.87[ASN][1000 genomes]
rs34407560	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34718679	0.84[AMR][1000 genomes]
rs34859729	0.93[ASN][1000 genomes]
rs34977427	0.83[ASN][1000 genomes]
rs35066133	0.84[ASN][1000 genomes]
rs35168204	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35204615	0.86[ASN][1000 genomes]
rs35210199	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35460138	0.86[ASN][1000 genomes]
rs35555888	0.86[ASN][1000 genomes]
rs35658945	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35769647	0.95[ASN][1000 genomes]
rs36125140	0.94[ASN][1000 genomes]
rs3794501	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4482214	0.83[EUR][1000 genomes]
rs4531679	0.87[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4774320	0.81[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4774321	0.81[AMR][1000 genomes]
rs4775110	0.95[CEU][hapmap];0.96[MEX][hapmap];0.85[AMR][1000 genomes]
rs4775111	0.82[AMR][1000 genomes]
rs4775114	0.92[ASN][1000 genomes]
rs4775115	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56375269	0.81[ASN][1000 genomes]
rs57361749	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57557135	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58087223	0.95[ASN][1000 genomes]
rs59282449	0.90[ASN][1000 genomes]
rs59514650	0.92[ASN][1000 genomes]
rs59540276	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60262196	0.96[ASN][1000 genomes]
rs60741546	0.95[ASN][1000 genomes]
rs61022867	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62002543	0.92[ASN][1000 genomes]
rs62002544	0.92[ASN][1000 genomes]
rs6494054	0.83[GIH][hapmap]
rs6494064	0.86[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap]
rs6494065	0.91[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap]
rs6494069	0.91[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs71480503	1.00[ASN][1000 genomes]
rs7168102	0.85[AMR][1000 genomes]
rs7173135	0.81[AMR][1000 genomes]
rs7175215	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7175246	0.81[AMR][1000 genomes]
rs7175490	0.81[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs7176281	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7176576	0.80[AMR][1000 genomes]
rs7178935	0.87[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs73418863	0.87[ASN][1000 genomes]
rs73418864	0.86[ASN][1000 genomes]
rs8027536	0.85[AMR][1000 genomes]
rs8028752	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.85[ASN][1000 genomes]
rs8029336	0.81[AMR][1000 genomes]
rs8030246	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8030323	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8031390	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8036907	0.85[EUR][1000 genomes]
rs8039514	0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8040456	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs8041221	0.95[CEU][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap]
rs8042516	0.81[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs877269	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9302206	0.81[CEU][hapmap]
rs9788719	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	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
3	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv904271	chr15:59249584-59393011	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv520872	chr15:59268410-59395184	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16940998	FAM63B	cis	parietal	SCAN
rs16940998	GCNT3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59344400-59392800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:59350800-59384600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:59354000-59390600	Strong transcription	Primary B cells from peripheral blood	blood
4	chr15:59354400-59396800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:59355400-59392800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr15:59355600-59378400	Strong transcription	Osteobl	bone
7	chr15:59355600-59392800	Strong transcription	Liver	Liver
8	chr15:59355600-59396600	Weak transcription	Fetal Heart	heart
9	chr15:59355800-59386800	Weak transcription	Stomach Mucosa	stomach
10	chr15:59359400-59396600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:59364800-59392600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:59365800-59390600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:59366400-59390600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:59367400-59390800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:59367600-59390200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:59367600-59390600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:59367800-59389800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:59368000-59379600	Strong transcription	Placenta	Placenta
19	chr15:59368000-59379800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:59368200-59378400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:59368200-59379600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:59368200-59389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr15:59368200-59390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:59368200-59392800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:59368600-59389800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:59370400-59383800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:59371600-59392800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:59371800-59389200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr15:59372000-59380000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:59372000-59380200	Strong transcription	GM12878-XiMat	blood
31	chr15:59372400-59386000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:59372400-59386000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:59372400-59390400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:59373000-59379000	Strong transcription	Fetal Muscle Leg	muscle
35	chr15:59373000-59379400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:59373000-59386000	Strong transcription	Fetal Intestine Large	intestine
37	chr15:59373000-59386000	Strong transcription	Fetal Thymus	thymus
38	chr15:59373000-59389200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr15:59373000-59389200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr15:59373000-59390400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr15:59373200-59378800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr15:59373200-59379400	Strong transcription	Hela-S3	cervix
43	chr15:59373200-59382800	Strong transcription	Primary T cells from cord blood	blood
44	chr15:59373200-59386000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:59373600-59378800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:59373600-59385000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:59373600-59387000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:59374000-59396800	Weak transcription	Ovary	ovary
49	chr15:59374200-59383800	Weak transcription	Lung	lung
50	chr15:59374200-59383800	Weak transcription	Psoas Muscle	Psoas

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