Variant report

Variant	rs12102209
Chromosome Location	chr15:41201699-41201700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41199759..41201940-chr15:41248954..41250742,2	K562	blood:
2	chr15:41201322..41202834-chr15:41232432..41234012,2	MCF-7	breast:
3	chr15:41195189..41208751-chr15:41218816..41225232,20	MCF-7	breast:
4	chr15:41197462..41204234-chr15:41215803..41223321,13	K562	blood:
5	chr15:41194927..41205036-chr15:41218861..41227276,20	MCF-7	breast:
6	chr15:41193987..41204234-chr15:41215915..41223506,12	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS18-1	chr15:41201027-41202517	XLOC_011223

No data

Variant related genes	Relation type
ENSG00000128917	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12102102	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16971183	0.82[YRI][hapmap]
rs59897077	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs61021048	0.89[AMR][1000 genomes]
rs7179443	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs8028214	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs880428	0.95[YRI][hapmap]
rs9744921	0.82[AFR][1000 genomes];0.87[AMR][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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
7	esv1819792	chr15:41184722-41234825	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41197400-41205600	Enhancers	Lung	lung
2	chr15:41199200-41201800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41199200-41202000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:41199200-41202400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:41199200-41204600	Enhancers	Liver	Liver
6	chr15:41199400-41206400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:41199600-41202000	Weak transcription	Fetal Kidney	kidney
8	chr15:41199600-41202200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:41199600-41202400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:41199600-41203200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:41199600-41203800	Weak transcription	Aorta	Aorta
12	chr15:41199600-41205000	Enhancers	Fetal Intestine Large	intestine
13	chr15:41199600-41205400	Enhancers	Fetal Muscle Leg	muscle
14	chr15:41199800-41201800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:41199800-41201800	Weak transcription	HSMMtube	muscle
16	chr15:41199800-41202000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:41199800-41202200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:41199800-41203200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:41199800-41203200	Enhancers	Fetal Muscle Trunk	muscle
20	chr15:41199800-41203400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr15:41199800-41204200	Enhancers	Fetal Intestine Small	intestine
22	chr15:41199800-41210000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr15:41200000-41201800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:41200000-41201800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr15:41200000-41201800	Weak transcription	Esophagus	oesophagus
26	chr15:41200000-41201800	Weak transcription	Pancreas	Pancrea
27	chr15:41200000-41203000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr15:41200000-41203200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr15:41200000-41203200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:41200000-41204200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:41200000-41204200	Weak transcription	NHEK	skin
32	chr15:41200000-41204400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:41200000-41204800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr15:41200000-41209400	Weak transcription	Fetal Brain Female	brain
35	chr15:41200200-41201800	Weak transcription	Small Intestine	intestine
36	chr15:41200200-41202000	Weak transcription	HMEC	breast
37	chr15:41200200-41202200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:41200200-41203800	Enhancers	Adipose Nuclei	Adipose
39	chr15:41200200-41209800	Weak transcription	Right Ventricle	heart
40	chr15:41200400-41201800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:41200400-41201800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:41200400-41202200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:41200400-41202400	Weak transcription	GM12878-XiMat	blood
44	chr15:41200400-41203000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:41200400-41203400	Weak transcription	HUVEC	blood vessel
46	chr15:41200400-41206600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:41200600-41201800	Weak transcription	Placenta	Placenta
48	chr15:41200600-41201800	Weak transcription	Right Atrium	heart
49	chr15:41200600-41202000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:41200600-41202000	Weak transcription	Gastric	stomach

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