Variant report

Variant	rs73309064
Chromosome Location	chr12:50195468-50195469
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr12:50195315-50195499	HepG2	liver:	n/a	n/a
2	ZNF263	chr12:50195266-50195839	HEK293-T-REx	kidney:	n/a	chr12:50195443-50195464 chr12:50195454-50195463
3	POLR2A	chr12:50195432-50195953	GM12878	blood:	n/a	n/a
4	FOXA2	chr12:50195173-50195696	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50184479..50186991-chr12:50194660..50197233,2	K562	blood:
2	chr12:50185305..50186991-chr12:50194287..50197233,2	K562	blood:
3	chr12:50190487..50192321-chr12:50194210..50195779,2	MCF-7	breast:
4	chr12:50194301..50195990-chr12:50198569..50200807,2	K562	blood:
5	chr12:50168739..50170709-chr12:50195433..50197562,2	K562	blood:
6	chr12:50170539..50173499-chr12:50194309..50196084,2	MCF-7	breast:
7	chr12:50193481..50196503-chr12:50223666..50226555,3	MCF-7	breast:

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10875977	1.00[ASN][1000 genomes]
rs11169164	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169165	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169171	1.00[ASN][1000 genomes]
rs12315844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321190	1.00[ASN][1000 genomes]
rs17123990	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56751503	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57832845	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61691368	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137037	1.00[ASN][1000 genomes]
rs7137262	1.00[ASN][1000 genomes]
rs7313739	1.00[ASN][1000 genomes]
rs73309047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73309054	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73309090	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73310907	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968164	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50174400-50209600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:50177800-50203400	Weak transcription	Fetal Kidney	kidney
3	chr12:50179200-50213600	Weak transcription	Hela-S3	cervix
4	chr12:50183200-50197600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:50183200-50200600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:50183200-50201400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:50183200-50203400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr12:50183400-50197600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr12:50183400-50200000	Strong transcription	Brain Hippocampus Middle	brain
10	chr12:50183400-50200000	Strong transcription	Brain Inferior Temporal Lobe	brain
11	chr12:50183400-50200200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:50183400-50200200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr12:50183400-50200600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:50183400-50200600	Strong transcription	Fetal Brain Female	brain
15	chr12:50183400-50202200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:50183400-50202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:50183400-50202600	Strong transcription	NHLF	lung
18	chr12:50183800-50199800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:50184400-50200000	Strong transcription	Lung	lung
20	chr12:50184400-50200000	Strong transcription	Spleen	Spleen
21	chr12:50184400-50200200	Strong transcription	Brain Germinal Matrix	brain
22	chr12:50184400-50203200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:50184600-50199800	Strong transcription	Brain Anterior Caudate	brain
24	chr12:50184800-50199800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:50185000-50202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:50185200-50196400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:50185200-50200000	Strong transcription	Gastric	stomach
28	chr12:50185200-50200200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:50185200-50200200	Strong transcription	Fetal Thymus	thymus
30	chr12:50185200-50200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:50185600-50201200	Strong transcription	Fetal Stomach	stomach
32	chr12:50185800-50199800	Strong transcription	Placenta	Placenta
33	chr12:50185800-50200400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:50186200-50200400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr12:50187000-50199800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:50187200-50203000	Strong transcription	Primary T cells from cord blood	blood
37	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:50188400-50200000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr12:50188800-50196800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:50188800-50199800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr12:50188800-50200200	Strong transcription	Thymus	Thymus
42	chr12:50189000-50196400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:50189000-50200000	Strong transcription	NHEK	skin
44	chr12:50189200-50199600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:50189200-50214600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:50189400-50200000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:50189800-50199600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:50189800-50200000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:50190000-50197600	Strong transcription	Ovary	ovary
50	chr12:50190000-50199200	Strong transcription	Aorta	Aorta

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