Variant report

Variant	rs2052805
Chromosome Location	chr15:58982987-58982988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58982751..58984795-chr15:59030172..59031707,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLTM-6	chr15:58982672-58985806	NR_073415

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs11071391	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs11071392	0.83[AMR][1000 genomes]
rs11071393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11071397	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs11853494	0.89[ASN][1000 genomes]
rs11856657	0.89[ASN][1000 genomes]
rs12437457	0.88[CEU][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs12437952	0.81[AMR][1000 genomes]
rs12437955	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437998	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438487	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12438810	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12439231	0.94[CEU][hapmap];0.83[AMR][1000 genomes]
rs12439632	0.81[CEU][hapmap]
rs12440091	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440246	0.85[AMR][1000 genomes]
rs12440267	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12441313	0.94[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12441912	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442451	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12442956	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591310	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs12592332	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12592750	0.85[AMR][1000 genomes]
rs12594742	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs12708455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901989	0.88[CEU][hapmap]
rs12905110	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12906705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12906714	0.94[CEU][hapmap];0.81[AMR][1000 genomes]
rs12907237	0.93[CEU][hapmap];0.81[AMR][1000 genomes]
rs12908165	0.89[ASW][hapmap];0.87[CEU][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes]
rs12908261	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908449	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12912286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs12912327	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913383	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs12917500	0.81[AMR][1000 genomes]
rs12917577	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs1365772	0.82[CHD][hapmap]
rs1426652	0.82[CEU][hapmap];0.89[GIH][hapmap]
rs1551445	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs16940587	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes]
rs16940589	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16940647	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs16940651	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs17236194	0.94[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs17301905	0.80[EUR][1000 genomes]
rs17301954	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1820548	0.80[ASN][1000 genomes]
rs1869133	0.80[CHD][hapmap];0.82[JPT][hapmap]
rs1869135	0.80[CHD][hapmap]
rs2052804	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081703	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs2305421	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs28455654	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28470809	0.83[AMR][1000 genomes]
rs28489732	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28536555	0.83[AMR][1000 genomes]
rs28542491	0.80[EUR][1000 genomes]
rs28549001	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28573205	0.85[AMR][1000 genomes]
rs28576281	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600144	0.80[ASN][1000 genomes]
rs28609304	0.80[EUR][1000 genomes]
rs28637832	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28639679	0.81[EUR][1000 genomes]
rs28678478	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28722857	0.83[AMR][1000 genomes]
rs28724298	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28818840	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35499736	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35956992	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs544282	0.85[ASN][1000 genomes]
rs6494030	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs6494031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6494032	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6494033	0.94[CEU][hapmap]
rs6494034	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6494038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7163733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7163939	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7165035	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7165402	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7166076	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7166325	0.94[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7167528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7169205	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs7170314	0.94[CEU][hapmap]
rs7174175	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7174386	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7174414	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7178954	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7180550	0.80[ASN][1000 genomes]
rs8026668	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8029301	0.84[GIH][hapmap]
rs8029805	0.94[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8033691	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8035960	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036005	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs8036448	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8039791	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap]
rs8040358	0.81[EUR][1000 genomes]
rs9302203	0.94[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes]
rs9635351	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs9920310	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9920720	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes]
rs9921024	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[ASN][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	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
4	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
5	nsv974583	chr15:58979010-58987450	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2052805	PIGB	cis	cerebellum	SCAN
rs2052805	RNF111	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
2	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:58936200-58991400	Weak transcription	HMEC	breast
4	chr15:58951200-58987000	Weak transcription	NHEK	skin
5	chr15:58955200-58988400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:58956600-58984400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:58956600-58984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:58957400-58984400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:58961600-58987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:58961800-58984600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:58962000-58986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:58962000-58987200	Weak transcription	Fetal Lung	lung
17	chr15:58968200-58984000	Weak transcription	Brain Germinal Matrix	brain
18	chr15:58968400-58987000	Weak transcription	Fetal Kidney	kidney
19	chr15:58969200-58984200	Weak transcription	Fetal Intestine Large	intestine
20	chr15:58970600-58987200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:58971800-58984800	Weak transcription	NHDF-Ad	bronchial
22	chr15:58971800-58986800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:58972000-58986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:58972400-58984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:58972600-58983000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:58972600-58983000	Weak transcription	Spleen	Spleen
27	chr15:58972600-58984400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:58972600-58984400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:58972600-58988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:58972600-58988800	Weak transcription	Fetal Stomach	stomach
31	chr15:58972600-58989000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:58973200-58984600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr15:58973200-58984800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:58973600-58984200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:58974600-58991000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:58975800-58989200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:58976800-58983200	Weak transcription	HSMMtube	muscle
38	chr15:58976800-58984200	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:58976800-58986400	Weak transcription	Gastric	stomach
40	chr15:58976800-58986600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:58977000-58984200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:58977000-58984400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr15:58977000-58984400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr15:58977000-58984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:58977000-58988600	Weak transcription	Fetal Intestine Small	intestine
46	chr15:58977000-58989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:58977200-58983000	Weak transcription	K562	blood
48	chr15:58977200-58983200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr15:58977200-58983600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:58977200-58983600	Weak transcription	GM12878-XiMat	blood

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