Variant report

Variant	rs12460178
Chromosome Location	chr19:45664890-45664891
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45664698-45665050	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:45663875-45665858	K562	blood:	n/a	n/a
3	SMC3	chr19:45664681-45665819	SK-N-SH	brain:	n/a	chr19:45665468-45665482 chr19:45665713-45665723
4	POLR2A	chr19:45663434-45665662	K562	blood:	n/a	n/a
5	NR2F2	chr19:45664113-45665215	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:45664651-45665196	HL-60	blood:	n/a	n/a
7	POLR2A	chr19:45664056-45665595	MCF-7	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45664088..45666150-chr19:45752306..45754556,2	K562	blood:
2	chr19:45664293..45670548-chr19:45677917..45684715,10	MCF-7	breast:
3	chr19:45664476..45666150-chr19:45681699..45683460,2	K562	blood:
4	chr19:45663246..45665913-chr19:45689234..45691618,2	MCF-7	breast:
5	chr19:45663965..45672033-chr19:45672145..45675901,9	K562	blood:
6	chr19:45664265..45666960-chr19:45670245..45671965,2	K562	blood:
7	chr19:45664797..45666644-chr19:45690247..45693088,2	K562	blood:
8	chr19:45664074..45668689-chr19:45680998..45684242,7	MCF-7	breast:
9	chr19:45662322..45668242-chr19:45680645..45684470,7	K562	blood:
10	chr19:45663488..45666150-chr19:45752160..45753806,2	K562	blood:
11	chr19:45662769..45665493-chr19:45847031..45849570,2	MCF-7	breast:

No data

Variant related genes	Relation type
NKPD1	TF binding region
ENSG00000267545	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000104892	Chromatin interaction
ENSG00000266958	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1048552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12459817	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12461733	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12463298	0.83[AMR][1000 genomes]
rs12463327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57302271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57627123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58504789	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59215448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60460304	1.00[AMR][1000 genomes]
rs6509200	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs73564216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564218	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73564265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS 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	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1795888	chr19:45650386-45681988	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1798099	chr19:45664218-45681988	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45657800-45668200	Weak transcription	Right Atrium	heart
2	chr19:45660200-45674000	Weak transcription	A549	lung
3	chr19:45662000-45667000	Weak transcription	Spleen	Spleen
4	chr19:45662400-45667200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:45662600-45666600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:45662600-45667600	Weak transcription	HUVEC	blood vessel
7	chr19:45662800-45669000	Enhancers	Esophagus	oesophagus
8	chr19:45663000-45665000	Bivalent Enhancer	Fetal Intestine Large	intestine
9	chr19:45663400-45665400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:45663400-45665400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr19:45663400-45665800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr19:45663600-45665400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:45663800-45665000	Bivalent Enhancer	Fetal Intestine Small	intestine
14	chr19:45663800-45665000	Enhancers	Gastric	stomach
15	chr19:45663800-45665000	Enhancers	Pancreas	Pancrea
16	chr19:45663800-45665200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr19:45663800-45665600	Enhancers	NHEK	skin
18	chr19:45664000-45665000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:45664000-45665000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
20	chr19:45664000-45665400	Enhancers	Lung	lung
21	chr19:45664000-45665400	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr19:45664000-45665400	Enhancers	HMEC	breast
23	chr19:45664000-45666400	Bivalent Enhancer	Colonic Mucosa	Colon
24	chr19:45664000-45667600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:45664000-45670200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr19:45664200-45665000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:45664200-45665400	Bivalent Enhancer	Fetal Muscle Leg	muscle
28	chr19:45664200-45667800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:45664200-45668400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:45664600-45665000	Bivalent Enhancer	HepG2	liver
31	chr19:45664600-45665200	Bivalent Enhancer	Placenta	Placenta
32	chr19:45664600-45665400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:45664600-45665600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
34	chr19:45664600-45667600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:45664800-45665400	Enhancers	Ovary	ovary
36	chr19:45664800-45665600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:45664800-45665800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr19:45664800-45666000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr19:45664800-45666400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr19:45664800-45666800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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