Variant report

Variant	rs12439534
Chromosome Location	chr15:31621985-31621986
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:31608249..31610861-chr15:31620080..31623099,3	K562	blood:
2	chr15:31608249..31610861-chr15:31620873..31623099,2	K562	blood:
3	chr15:31618267..31621353-chr15:31621763..31625829,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169926	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11070922	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070938	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630449	0.85[AFR][1000 genomes]
rs12439925	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12595077	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899315	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2004566	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2338700	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2338701	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2879243	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34784107	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779516	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4779858	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4779859	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175141	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8039367	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv932896	chr15:31292475-31730445	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv903838	chr15:31452911-31672128	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv1815415	chr15:31483843-31697213	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34100	chr15:31496514-31792591	Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv456747	chr15:31537496-31637996	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv568772	chr15:31537496-31637996	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv903840	chr15:31589970-31800149	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	esv1839818	chr15:31594828-31637996	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv542318	chr15:31601016-31628938	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv1050482	chr15:31601016-31672921	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv542319	chr15:31605961-31628938	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1048082	chr15:31610245-31667000	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv1045944	chr15:31610245-31672921	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
17	nsv516681	chr15:31616674-31675453	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS 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	13 gene(s)	inside rSNPs	diseases
18	nsv903841	chr15:31616674-31697242	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
19	esv3487683	chr15:31617885-31622158	Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
20	esv3487684	chr15:31617885-31622158	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
21	esv3358300	chr15:31618685-31622033	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
22	nsv903842	chr15:31621321-31697242	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
23	nsv456748	chr15:31621321-31697642	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
24	nsv568801	chr15:31621321-31697642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31617400-31622000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr15:31617400-31622000	Active TSS	Esophagus	oesophagus
3	chr15:31617400-31622400	Active TSS	Gastric	stomach
4	chr15:31617600-31622000	Active TSS	Brain Angular Gyrus	brain
5	chr15:31617600-31622000	Active TSS	Fetal Intestine Small	intestine
6	chr15:31617600-31622200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:31617600-31622200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr15:31617600-31622200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr15:31617800-31622000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr15:31617800-31622000	Active TSS	Brain Cingulate Gyrus	brain
11	chr15:31617800-31622000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:31617800-31622000	Active TSS	Fetal Brain Female	brain
13	chr15:31617800-31622000	Active TSS	Pancreas	Pancrea
14	chr15:31617800-31622200	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr15:31617800-31622600	Active TSS	Rectal Smooth Muscle	rectum
16	chr15:31618000-31622000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr15:31619000-31622200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:31619200-31622400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr15:31620400-31622200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr15:31620400-31622200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:31620600-31622200	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr15:31620800-31622000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:31620800-31622400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr15:31620800-31622400	Flanking Active TSS	Liver	Liver
25	chr15:31620800-31623200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr15:31620800-31632600	Enhancers	Fetal Heart	heart
27	chr15:31621000-31622000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr15:31621000-31622000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:31621000-31622400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:31621000-31622400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr15:31621000-31622600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr15:31621000-31622600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr15:31621000-31622600	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr15:31621000-31623000	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr15:31621000-31624000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr15:31621000-31624600	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr15:31621000-31624800	Weak transcription	Ovary	ovary
38	chr15:31621000-31626600	Transcr. at gene 5' and 3'	Thymus	Thymus
39	chr15:31621200-31622000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr15:31621200-31622200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:31621200-31622200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr15:31621200-31622200	Enhancers	Placenta Amnion	Placenta Amnion
43	chr15:31621200-31622400	Flanking Active TSS	Right Ventricle	heart
44	chr15:31621200-31622400	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr15:31621200-31622600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:31621200-31622800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:31621200-31623000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:31621200-31623200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:31621200-31623200	Flanking Active TSS	Colonic Mucosa	Colon
50	chr15:31621400-31622000	Flanking Active TSS	Stomach Mucosa	stomach

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