Variant report

Variant	rs12050904
Chromosome Location	chr15:99925406-99925407
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99925089..99927995-chr15:99937922..99942440,4	K562	blood:

Variant related genes	Relation type
ENSG00000259760	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11247085	0.95[ASN][1000 genomes]
rs11858067	0.82[JPT][hapmap]
rs12050640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2175226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28736849	0.95[ASN][1000 genomes]
rs3817147	0.83[JPT][hapmap]
rs3920191	0.82[JPT][hapmap]
rs56033877	0.98[ASN][1000 genomes]
rs6598239	0.91[ASN][1000 genomes]
rs6598240	0.81[AMR][1000 genomes]
rs7162764	0.83[JPT][hapmap]
rs7176559	0.91[ASN][1000 genomes]
rs7181449	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[ASN][1000 genomes]
rs7183514	0.85[JPT][hapmap]
rs74033472	0.93[ASN][1000 genomes]
rs74033475	0.95[ASN][1000 genomes]
rs978704	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking 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	31 gene(s)	inside rSNPs	diseases
6	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
11	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99867200-99926600	Weak transcription	NHEK	skin
2	chr15:99886600-99931400	Weak transcription	Esophagus	oesophagus
3	chr15:99902000-99925600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:99903600-99926600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:99905000-99928200	Weak transcription	Pancreas	Pancrea
6	chr15:99907200-99926600	Weak transcription	Fetal Kidney	kidney
7	chr15:99907400-99926200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:99907400-99928200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:99909800-99926200	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:99910400-99934400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:99915200-99947400	Weak transcription	Thymus	Thymus
12	chr15:99916800-99931200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr15:99923000-99926200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:99923000-99927600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:99923000-99928400	Weak transcription	Brain Angular Gyrus	brain
16	chr15:99923200-99930800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr15:99923400-99927000	Weak transcription	Aorta	Aorta
18	chr15:99923400-99928600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:99923600-99927400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:99923800-99925600	Weak transcription	Adipose Nuclei	Adipose
21	chr15:99924200-99925800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:99924200-99927400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr15:99924200-99928400	Weak transcription	Brain Substantia Nigra	brain
24	chr15:99924600-99925600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:99924600-99925600	Enhancers	Psoas Muscle	Psoas
26	chr15:99924800-99925600	Strong transcription	Primary hematopoietic stem cells	blood
27	chr15:99924800-99926200	Enhancers	Primary T cells from cord blood	blood
28	chr15:99924800-99926800	Enhancers	Right Atrium	heart
29	chr15:99924800-99926800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr15:99924800-99927000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:99924800-99927000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:99924800-99927000	Genic enhancers	Fetal Intestine Small	intestine
33	chr15:99924800-99927800	Enhancers	Ovary	ovary
34	chr15:99925000-99925600	Enhancers	Placenta	Placenta
35	chr15:99925000-99925600	Enhancers	Spleen	Spleen
36	chr15:99925000-99925800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr15:99925000-99925800	Genic enhancers	Fetal Intestine Large	intestine
38	chr15:99925000-99926200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:99925000-99926800	Enhancers	Small Intestine	intestine
40	chr15:99925000-99926800	Genic enhancers	Dnd41	blood
41	chr15:99925000-99927000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:99925000-99927000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr15:99925000-99927000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr15:99925000-99927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:99925200-99925600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr15:99925200-99925600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:99925200-99925600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:99925200-99925600	Enhancers	Colonic Mucosa	Colon
49	chr15:99925200-99925600	Genic enhancers	Fetal Stomach	stomach
50	chr15:99925200-99925600	Flanking Active TSS	HepG2	liver

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