Variant report

Variant	rs12050786
Chromosome Location	chr15:59946923-59946924
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:59903703..59905876-chr15:59946460..59948688,2	K562	blood:
2	chr15:59945879..59953077-chr15:59978622..59984049,13	K562	blood:
3	chr15:59946363..59951356-chr15:59979923..59984049,7	K562	blood:

Variant related genes	Relation type
ENSG00000259238	Chromatin interaction
ENSG00000140297	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12161947	0.85[EUR][1000 genomes]
rs12161992	0.85[EUR][1000 genomes]
rs12161993	0.85[EUR][1000 genomes]
rs16941544	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17236713	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17236734	0.95[EUR][1000 genomes]
rs17302448	0.95[EUR][1000 genomes]
rs17302608	0.90[EUR][1000 genomes]
rs2306359	0.81[EUR][1000 genomes]
rs28395445	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28418513	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs28422085	0.95[EUR][1000 genomes]
rs28437066	0.95[EUR][1000 genomes]
rs28642859	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28654927	0.90[EUR][1000 genomes]
rs28883924	0.90[EUR][1000 genomes]
rs2899650	0.85[EUR][1000 genomes]
rs4775192	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4775193	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4775198	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151443	0.85[EUR][1000 genomes]
rs6151457	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6151492	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151497	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6151505	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6151522	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151534	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6151538	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151540	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6151567	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6151575	0.95[EUR][1000 genomes]
rs6151591	0.95[EUR][1000 genomes]
rs8027421	0.90[EUR][1000 genomes]
rs8033208	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8033718	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
7	nsv1043693	chr15:59944471-59971500	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
2	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:59926600-59947600	Weak transcription	Right Ventricle	heart
4	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
5	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
6	chr15:59929000-59947200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr15:59929200-59947600	Weak transcription	Ovary	ovary
8	chr15:59930600-59948200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:59932800-59947800	Weak transcription	Colonic Mucosa	Colon
10	chr15:59932800-59948000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:59936000-59948000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:59936400-59947000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:59936600-59947000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:59937400-59947600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:59938200-59947600	Weak transcription	Spleen	Spleen
16	chr15:59938200-59947800	Weak transcription	NHLF	lung
17	chr15:59938200-59948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:59938600-59949200	Weak transcription	Lung	lung
19	chr15:59938800-59947400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:59941000-59949200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:59941200-59947600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:59941200-59948000	Weak transcription	Fetal Stomach	stomach
23	chr15:59941600-59947400	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr15:59943000-59947600	Weak transcription	Fetal Heart	heart
25	chr15:59943000-59948200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:59944200-59948000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:59944200-59948200	Weak transcription	Fetal Intestine Small	intestine
28	chr15:59944400-59947400	Weak transcription	Stomach Mucosa	stomach
29	chr15:59944400-59947600	Weak transcription	Brain Substantia Nigra	brain
30	chr15:59944400-59947800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:59944400-59947800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr15:59944400-59947800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:59944400-59947800	Weak transcription	HUVEC	blood vessel
34	chr15:59944400-59948000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:59944400-59948000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:59944600-59947200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:59944600-59947600	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:59944600-59947600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:59944600-59947800	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:59944600-59948000	Weak transcription	Fetal Brain Male	brain
41	chr15:59944600-59948000	Weak transcription	Fetal Brain Female	brain
42	chr15:59944600-59948000	Weak transcription	Osteobl	bone
43	chr15:59944600-59948400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:59945000-59947000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:59945000-59947200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:59945000-59947600	Weak transcription	Brain Anterior Caudate	brain
47	chr15:59945000-59947600	Weak transcription	NHDF-Ad	bronchial
48	chr15:59945000-59947800	Weak transcription	HMEC	breast
49	chr15:59945000-59948000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:59945000-59948000	Weak transcription	NH-A	brain

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