Variant report

Variant	rs12439632
Chromosome Location	chr15:59103963-59103964
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs11071393	0.81[CEU][hapmap]
rs11071397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12437928	0.86[JPT][hapmap]
rs12437952	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12439231	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes]
rs12441313	0.87[CEU][hapmap];0.95[CHB][hapmap]
rs12441912	0.85[CEU][hapmap];0.94[CHB][hapmap]
rs12442451	0.87[CEU][hapmap]
rs12591310	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592332	0.80[CEU][hapmap]
rs12594742	0.81[CEU][hapmap]
rs12595057	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708455	0.81[CEU][hapmap]
rs12901817	0.82[ASN][1000 genomes]
rs12905110	0.81[CEU][hapmap];0.95[CHB][hapmap]
rs12906705	0.81[CEU][hapmap]
rs12906714	0.87[CEU][hapmap];0.95[CHB][hapmap]
rs12907237	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs12908261	0.87[CEU][hapmap];0.95[CHB][hapmap]
rs12912286	0.81[CEU][hapmap]
rs12913383	0.94[CEU][hapmap]
rs12914164	0.81[JPT][hapmap]
rs12915713	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12917083	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12917577	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs1426652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1551445	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678977	0.82[ASN][1000 genomes]
rs16940651	0.81[CEU][hapmap]
rs17236194	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs2013098	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2052805	0.81[CEU][hapmap]
rs2620360	0.82[ASN][1000 genomes]
rs28394222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412567	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28470809	0.81[AMR][1000 genomes]
rs28470867	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28510910	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28536555	0.81[AMR][1000 genomes]
rs28549775	0.80[ASN][1000 genomes]
rs28701980	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs28733370	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28793354	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28800895	0.96[ASN][1000 genomes]
rs28812884	0.82[ASN][1000 genomes]
rs28876251	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28889637	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34362744	0.82[ASN][1000 genomes]
rs347112	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4775095	0.86[JPT][hapmap]
rs481309	0.86[JPT][hapmap]
rs500057	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs501165	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs510759	0.86[JPT][hapmap]
rs556256	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs574683	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs597112	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs601795	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs62002455	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62002456	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494030	0.81[CEU][hapmap]
rs6494031	0.81[CEU][hapmap]
rs6494034	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs6494038	0.81[CEU][hapmap]
rs652193	0.86[JPT][hapmap]
rs654857	0.82[ASN][1000 genomes]
rs654870	0.82[ASN][1000 genomes]
rs664936	0.80[JPT][hapmap]
rs684505	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs688343	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7163733	0.81[CEU][hapmap]
rs7165019	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165402	0.81[CEU][hapmap]
rs7166325	0.81[CEU][hapmap]
rs7167528	0.81[CEU][hapmap]
rs7168825	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7169205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169796	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7171482	0.89[EUR][1000 genomes]
rs8025383	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8029301	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8029805	0.87[CEU][hapmap];0.94[CHB][hapmap]
rs8033691	0.87[CEU][hapmap];0.95[CHB][hapmap]
rs8036005	0.81[CEU][hapmap]
rs9635351	0.81[CEU][hapmap]
rs9921024	0.80[CEU][hapmap]

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	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	44 gene(s)	inside rSNPs	diseases
4	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59064600-59145600	Weak transcription	Gastric	stomach
2	chr15:59065200-59117800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:59065800-59142800	Weak transcription	Aorta	Aorta
4	chr15:59067000-59157800	Weak transcription	Hela-S3	cervix
5	chr15:59067400-59111400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:59067800-59105000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr15:59069600-59106000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:59069600-59119000	Weak transcription	Fetal Brain Male	brain
9	chr15:59069800-59121400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr15:59072000-59105600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:59075000-59139800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:59077800-59122000	Weak transcription	Brain Substantia Nigra	brain
13	chr15:59077800-59153600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:59086200-59125800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:59086400-59125800	Weak transcription	Right Ventricle	heart
16	chr15:59087200-59104600	Weak transcription	HMEC	breast
17	chr15:59088400-59119200	Weak transcription	Colonic Mucosa	Colon
18	chr15:59088600-59105400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:59090200-59156600	Weak transcription	Small Intestine	intestine
20	chr15:59090400-59105200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:59090400-59121600	Weak transcription	Fetal Heart	heart
22	chr15:59094200-59122800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:59095200-59156800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr15:59096200-59105200	Weak transcription	Osteobl	bone
25	chr15:59097000-59110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr15:59100200-59105000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:59100200-59105200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:59100400-59122200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:59100400-59139800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr15:59100600-59104600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:59100600-59105600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:59101200-59106000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:59101800-59104000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr15:59101800-59106000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:59101800-59107600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:59101800-59112400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:59102000-59104000	Strong transcription	NHLF	lung
38	chr15:59102000-59104800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:59102000-59105800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr15:59102000-59108200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:59102000-59109200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:59102000-59126400	Weak transcription	Stomach Mucosa	stomach
43	chr15:59102200-59104000	Strong transcription	Fetal Brain Female	brain
44	chr15:59102400-59104000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:59102400-59104000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:59102400-59104000	Strong transcription	Primary T cells from cord blood	blood
47	chr15:59102400-59104000	Strong transcription	Liver	Liver
48	chr15:59102400-59104000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr15:59102400-59104000	Strong transcription	Rectal Smooth Muscle	rectum
50	chr15:59102400-59104000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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