Variant report

Variant	rs12439231
Chromosome Location	chr15:59025595-59025596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59025413..59026960-chr15:59029067..59030744,2	K562	blood:
2	chr15:59024558..59027557-chr15:59042098..59043745,2	K562	blood:
3	chr15:59025073..59028168-chr15:59040901..59043745,3	K562	blood:
4	chr15:59023017..59026002-chr15:59026211..59028184,2	K562	blood:

Variant related genes	Relation type
ENSG00000137845	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs11071391	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11071393	0.94[CEU][hapmap]
rs11071397	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs12437457	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12437952	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12437998	0.81[AMR][1000 genomes]
rs12438487	0.83[CEU][hapmap]
rs12439632	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[AMR][1000 genomes]
rs12440267	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12441912	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]
rs12442451	1.00[CEU][hapmap]
rs12591310	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12592332	0.94[CEU][hapmap]
rs12594742	0.88[CEU][hapmap]
rs12595057	0.82[AMR][1000 genomes]
rs12708455	0.94[CEU][hapmap]
rs12900343	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901989	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12905110	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12906705	0.94[CEU][hapmap]
rs12906714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12907237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12908165	0.80[CEU][hapmap]
rs12908261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12910927	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912286	0.94[CEU][hapmap]
rs12912327	0.84[AMR][1000 genomes]
rs12913383	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12917083	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12917577	0.88[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1426652	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1551445	0.88[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap]
rs16940587	0.88[CEU][hapmap]
rs16940589	0.88[CEU][hapmap]
rs16940647	0.83[CEU][hapmap]
rs16940651	0.88[CEU][hapmap]
rs17236194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17301954	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1820480	0.81[AMR][1000 genomes]
rs2013098	0.81[AMR][1000 genomes]
rs2052805	0.94[CEU][hapmap];0.83[AMR][1000 genomes]
rs2305421	0.94[CEU][hapmap]
rs2414608	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28394222	0.81[AMR][1000 genomes]
rs28412567	0.81[AMR][1000 genomes]
rs28455654	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs28470809	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28470867	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28489732	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28510910	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28536555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28549001	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28733370	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28793354	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28818840	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28876251	0.81[AMR][1000 genomes]
rs28889637	0.81[AMR][1000 genomes]
rs35956992	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6074	0.82[CEU][hapmap]
rs6494030	0.88[CEU][hapmap]
rs6494031	0.94[CEU][hapmap]
rs6494033	0.83[CEU][hapmap]
rs6494034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6494038	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs7163733	0.94[CEU][hapmap]
rs7163939	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165019	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7165035	0.83[CEU][hapmap]
rs7165402	0.88[CEU][hapmap]
rs7166076	0.83[CEU][hapmap]
rs7166325	0.88[CEU][hapmap]
rs7167528	0.94[CEU][hapmap]
rs7168825	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7169205	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7169796	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7170314	0.83[CEU][hapmap]
rs7174386	0.87[CEU][hapmap]
rs7174414	0.87[CEU][hapmap]
rs8025383	0.80[ASN][1000 genomes]
rs8029301	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs8029805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8036005	0.88[CEU][hapmap]
rs8039791	0.83[CEU][hapmap]
rs9302203	0.83[CEU][hapmap]
rs9635351	0.88[CEU][hapmap]
rs9920720	0.83[CEU][hapmap]
rs9921024	0.88[CEU][hapmap]

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	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
4	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
5	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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:59007400-59026400	Weak transcription	Fetal Intestine Large	intestine
3	chr15:59008600-59028400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:59009600-59029600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr15:59009800-59035400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:59010800-59031200	Weak transcription	Dnd41	blood
7	chr15:59013200-59030200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:59013400-59029800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:59016800-59034200	Weak transcription	Brain Germinal Matrix	brain
10	chr15:59017200-59027400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:59017200-59034400	Weak transcription	Fetal Kidney	kidney
12	chr15:59017400-59029000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:59021000-59025600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr15:59021600-59025600	Enhancers	Left Ventricle	heart
15	chr15:59021600-59025800	Enhancers	Placenta Amnion	Placenta Amnion
16	chr15:59021800-59029000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:59021800-59029600	Weak transcription	Fetal Lung	lung
18	chr15:59022000-59029600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:59022200-59025800	Enhancers	Brain Cingulate Gyrus	brain
20	chr15:59022200-59025800	Enhancers	HSMMtube	muscle
21	chr15:59022200-59040200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr15:59022400-59025600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr15:59022400-59025800	Enhancers	Brain Angular Gyrus	brain
24	chr15:59022400-59025800	Enhancers	Brain Hippocampus Middle	brain
25	chr15:59022400-59026800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr15:59022400-59029400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:59022600-59025600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr15:59022600-59034800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:59022600-59038600	Weak transcription	Fetal Brain Female	brain
30	chr15:59022800-59025800	Genic enhancers	Thymus	Thymus
31	chr15:59022800-59029600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:59023000-59026000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:59023000-59027000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr15:59023000-59030400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr15:59023200-59025600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:59023400-59025600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:59023400-59025800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr15:59023600-59025600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:59023600-59025600	Enhancers	Esophagus	oesophagus
40	chr15:59023600-59025600	Enhancers	Placenta	Placenta
41	chr15:59023600-59025800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:59023600-59026000	Enhancers	Stomach Mucosa	stomach
43	chr15:59023600-59027000	Weak transcription	Fetal Intestine Small	intestine
44	chr15:59023600-59027200	Enhancers	NHEK	skin
45	chr15:59023600-59040000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr15:59023800-59025600	Enhancers	NHDF-Ad	bronchial
47	chr15:59023800-59025800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr15:59023800-59026600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:59023800-59027200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:59023800-59028600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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