Variant report

Variant	rs798125
Chromosome Location	chr15:31116800-31116801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1043742	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1056118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1088473	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1105541	0.80[EUR][1000 genomes]
rs11293	1.00[JPT][hapmap]
rs11629793	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11630637	1.00[CHB][hapmap]
rs11632229	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11633786	1.00[CHB][hapmap]
rs11635775	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11636942	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11637469	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs12148903	0.91[EUR][1000 genomes]
rs12917508	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1474380	1.00[JPT][hapmap];0.82[TSI][hapmap]
rs16956447	1.00[JPT][hapmap]
rs16956455	1.00[JPT][hapmap]
rs1852035	0.81[EUR][1000 genomes]
rs1917421	0.81[EUR][1000 genomes]
rs1983459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2001686	0.80[EUR][1000 genomes]
rs2177670	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2293317	1.00[JPT][hapmap]
rs2339044	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2339045	0.80[AFR][1000 genomes]
rs2339114	0.82[EUR][1000 genomes]
rs2524998	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2691683	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28664821	0.88[EUR][1000 genomes]
rs2955777	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2955797	1.00[JPT][hapmap]
rs2959036	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2959037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3122	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34218876	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34520008	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35098644	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3512	1.00[JPT][hapmap]
rs35639533	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36047941	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3817498	1.00[JPT][hapmap]
rs4556757	0.81[EUR][1000 genomes]
rs4779496	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4779497	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4779498	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4779759	1.00[CHB][hapmap]
rs4779762	1.00[CHB][hapmap]
rs4779776	1.00[CHB][hapmap]
rs4779785	1.00[CHB][hapmap]
rs4779790	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62000188	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs711224	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7166258	1.00[CHB][hapmap]
rs7168641	1.00[JPT][hapmap]
rs7171208	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7176569	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7179234	1.00[JPT][hapmap]
rs798080	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798084	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798086	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs798127	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028173	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8031106	1.00[CHB][hapmap]
rs8034856	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs8035703	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8036176	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758374	chr15:30292944-31152491	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	esv2760022	chr15:30292944-31177476	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv903757	chr15:30369153-31179534	Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1052897	chr15:30501813-31184303	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
6	esv2757593	chr15:30605836-31177476	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv568751	chr15:30899133-31117403	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv903822	chr15:30899133-31165955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv903825	chr15:30918248-31116800	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv903827	chr15:30927210-31116800	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv568760	chr15:30936285-31117403	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv456744	chr15:30936285-31123235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv568761	chr15:30936285-31123235	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
16	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
17	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
18	nsv832950	chr15:30954625-31146464	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1044683	chr15:30954725-31183908	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv542300	chr15:30954725-31183908	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv529701	chr15:30954726-31183907	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
22	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
23	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
24	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
25	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
26	nsv903833	chr15:31088443-31174687	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv984044	chr15:31114428-31126547	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs798125	SNORD115-4	cis	parietal	SCAN
rs798125	RP11-540B6.2	cis	Whole Blood	GTEx
rs798125	GABRB3	cis	parietal	SCAN
rs798125	RP11-540B6.3	cis	lung	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31110200-31118200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:31114400-31125000	Weak transcription	Pancreas	Pancrea
3	chr15:31115600-31116800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:31115600-31116800	Active TSS	Primary T cells fromperipheralblood	blood
5	chr15:31115800-31116800	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr15:31115800-31116800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:31115800-31117200	Active TSS	NH-A	brain
8	chr15:31116000-31116800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:31116000-31116800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:31116000-31116800	Active TSS	HSMMtube	muscle
11	chr15:31116000-31120200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:31116200-31116800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:31116200-31117200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:31116200-31117200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:31116200-31118200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:31116200-31120200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:31116200-31120600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:31116200-31125400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:31116200-31125400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:31116200-31125800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:31116200-31126200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr15:31116200-31126600	Weak transcription	Brain Anterior Caudate	brain
23	chr15:31116200-31128000	Weak transcription	Fetal Brain Female	brain
24	chr15:31116200-31129800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:31116200-31131000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:31116200-31133600	Weak transcription	Osteobl	bone
27	chr15:31116200-31134200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr15:31116200-31135400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:31116200-31135400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:31116200-31136600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:31116400-31117000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:31116400-31120200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:31116400-31125000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr15:31116400-31126600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:31116400-31130600	Weak transcription	Placenta	Placenta
36	chr15:31116400-31135000	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr15:31116600-31116800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:31116600-31116800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr15:31116600-31116800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:31116600-31116800	Flanking Active TSS	Dnd41	blood
41	chr15:31116600-31117000	Active TSS	HSMM	muscle
42	chr15:31116600-31117600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr15:31116600-31120200	Weak transcription	Hela-S3	cervix
44	chr15:31116800-31117000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr15:31116800-31117000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:31116800-31117200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr15:31116800-31117200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr15:31116800-31117200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr15:31116800-31117400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:31116800-31117400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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