Variant report

Variant	rs12441912
Chromosome Location	chr15:58993694-58993695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11071391	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs11071393	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs11071397	0.86[CEU][hapmap];0.93[CHB][hapmap]
rs12437457	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes]
rs12437952	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12437955	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12437998	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12438487	0.81[CEU][hapmap]
rs12439231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12439632	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs12440091	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12440246	0.81[AMR][1000 genomes]
rs12440267	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442451	1.00[CEU][hapmap]
rs12442956	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12591310	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs12592332	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs12592750	0.81[AMR][1000 genomes]
rs12594742	0.86[CEU][hapmap]
rs12708455	0.93[CEU][hapmap]
rs12900343	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12901989	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs12905110	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12906705	0.93[CEU][hapmap]
rs12906714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs12907237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs12908165	0.86[CEU][hapmap]
rs12908261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908449	0.83[AMR][1000 genomes]
rs12912286	0.93[CEU][hapmap]
rs12912327	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12913383	0.80[CEU][hapmap]
rs12917083	0.83[AMR][1000 genomes]
rs12917500	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12917577	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs1426652	0.86[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1551445	0.86[CEU][hapmap];0.86[CHB][hapmap]
rs16940587	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs16940589	0.86[CEU][hapmap]
rs16940647	0.81[CEU][hapmap]
rs16940651	0.86[CEU][hapmap]
rs17236194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17301954	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052804	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2052805	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2305421	0.93[CEU][hapmap];0.84[AMR][1000 genomes]
rs2414608	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28455654	0.93[CEU][hapmap];0.92[AMR][1000 genomes]
rs28470809	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28489732	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28536555	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28549001	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28573205	0.81[AMR][1000 genomes]
rs28576281	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28637832	0.81[AMR][1000 genomes]
rs28678478	0.81[AMR][1000 genomes]
rs28722857	0.86[AMR][1000 genomes]
rs28724298	0.81[AMR][1000 genomes]
rs28818840	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35499736	0.89[AMR][1000 genomes]
rs35956992	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494030	0.86[CEU][hapmap]
rs6494031	0.93[CEU][hapmap]
rs6494033	0.81[CEU][hapmap]
rs6494034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494038	0.93[CEU][hapmap]
rs7163733	0.93[CEU][hapmap]
rs7163939	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165402	0.86[CEU][hapmap]
rs7166076	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs7166325	0.86[CEU][hapmap]
rs7167528	0.93[CEU][hapmap];0.92[AMR][1000 genomes]
rs7169205	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap]
rs7170314	0.81[CEU][hapmap]
rs7174386	0.86[CEU][hapmap]
rs7174414	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs8029301	0.93[CHB][hapmap]
rs8029805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8033691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036005	0.86[CEU][hapmap]
rs8036448	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8039791	0.80[CEU][hapmap]
rs9302203	0.81[CEU][hapmap]
rs9635351	0.86[CEU][hapmap];0.84[AMR][1000 genomes]
rs9920720	0.81[CEU][hapmap]
rs9921024	0.85[CEU][hapmap];0.83[AMR][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	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	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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-58996400	Weak transcription	NHLF	lung
2	chr15:58977200-58998200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:58977200-59004400	Weak transcription	Ovary	ovary
4	chr15:58977200-59007800	Weak transcription	HepG2	liver
5	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:58982400-59005000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:58982600-59008000	Weak transcription	Fetal Brain Male	brain
8	chr15:58983200-59016600	Weak transcription	Small Intestine	intestine
9	chr15:58985200-59005000	Weak transcription	HSMMtube	muscle
10	chr15:58985600-58995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:58986600-59016600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:58987400-59012000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:58987600-58995800	Weak transcription	Hela-S3	cervix
14	chr15:58987600-59005000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:58987600-59007800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:58989000-58997200	ZNF genes & repeats	GM12878-XiMat	blood
17	chr15:58989400-58996000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:58989800-58994200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:58989800-59016800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr15:58990000-58994000	Weak transcription	Psoas Muscle	Psoas
21	chr15:58990000-58994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:58990000-58996000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:58990000-58996000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:58990000-58996200	Weak transcription	Right Atrium	heart
25	chr15:58990000-58997600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:58990000-58998400	Weak transcription	Gastric	stomach
27	chr15:58990000-58998400	Weak transcription	Right Ventricle	heart
28	chr15:58990000-58998800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:58990000-59004800	Weak transcription	Pancreas	Pancrea
30	chr15:58990000-59005000	Weak transcription	Spleen	Spleen
31	chr15:58990000-59005200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:58990000-59023400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:58990200-58993800	Weak transcription	Stomach Mucosa	stomach
34	chr15:58990200-58994400	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr15:58990200-58995800	Weak transcription	Left Ventricle	heart
36	chr15:58990200-58996000	Weak transcription	Lung	lung
37	chr15:58990800-58994600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr15:58990800-58995800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:58991000-58994600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:58991400-58996400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:58991600-58994000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:58991600-58996800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:58991600-59005200	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:58991800-59005000	Weak transcription	Liver	Liver
45	chr15:58991800-59005000	Weak transcription	Fetal Kidney	kidney
46	chr15:58991800-59005000	Weak transcription	HMEC	breast
47	chr15:58991800-59012200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr15:58992000-58995800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr15:58992000-58996000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:58992000-58996600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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