Variant report

Variant	rs12625948
Chromosome Location	chr20:23336892-23336893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr20:23336748-23337197	A549	lung:	n/a	n/a
2	POLR2A	chr20:23336781-23339672	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr20:23335134-23339112	K562	blood:	n/a	n/a
4	POLR2A	chr20:23336808-23337158	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:23336572-23337229	GM12891	blood:	n/a	n/a
6	POLR2A	chr20:23336827-23337159	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr20:23336309-23337185	GM12892	blood:	n/a	n/a
8	POLR2A	chr20:23336475-23337251	K562	blood:	n/a	n/a
9	POLR2A	chr20:23336830-23337203	A549	lung:	n/a	n/a
10	POLR2A	chr20:23336617-23340019	IMR90	lung:	n/a	n/a
11	POLR2A	chr20:23335434-23337891	A549	lung:	n/a	n/a
12	POLR2A	chr20:23336476-23337127	GM12891	blood:	n/a	n/a
13	POLR2A	chr20:23336833-23337220	K562	blood:	n/a	n/a
14	POLR2A	chr20:23336784-23337189	A549	lung:	n/a	n/a
15	POLR2A	chr20:23336816-23337180	A549	lung:	n/a	n/a
16	POLR2A	chr20:23336211-23337248	GM12878	blood:	n/a	n/a
17	POLR2A	chr20:23336813-23337169	GM12878	blood:	n/a	n/a
18	POLR2A	chr20:23335979-23339442	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr20:23336831-23337152	MCF-7	breast:	n/a	n/a
20	POLR2A	chr20:23335466-23338042	HepG2	liver:	n/a	n/a
21	POLR2A	chr20:23336694-23337244	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr20:23336160-23339252	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr20:23336733-23337260	GM12892	blood:	n/a	n/a
24	POLR2A	chr20:23336890-23337120	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr20:23336789-23337236	HL-60	blood:	n/a	n/a
26	POLR2A	chr20:23335690-23337958	GM12878	blood:	n/a	n/a
27	POLR2A	chr20:23335851-23337807	HepG2	liver:	n/a	n/a
28	POLR2A	chr20:23336881-23337120	HepG2	liver:	n/a	n/a
29	POLR2A	chr20:23336157-23337218	HepG2	liver:	n/a	n/a
30	POLR2A	chr20:23336665-23337157	GM12878	blood:	n/a	n/a
31	POLR2A	chr20:23336806-23337191	GM12878	blood:	n/a	n/a
32	POLR2A	chr20:23335992-23339760	GM12891	blood:	n/a	n/a
33	POLR2A	chr20:23336677-23337211	GM12891	blood:	n/a	n/a
34	POLR2A	chr20:23336574-23338181	GM12892	blood:	n/a	n/a
35	POLR2A	chr20:23335995-23339278	PFSK-1	brain:	n/a	n/a
36	POLR2A	chr20:23335386-23339511	GM12878	blood:	n/a	n/a
37	POLR2A	chr20:23336838-23337164	A549	lung:	n/a	n/a
38	RAD21	chr20:23336762-23337272	H1-hESC	embryonic stem cell:	n/a	chr20:23337193-23337205

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23336285..23337868-chr20:23382600..23384693,2	MCF-7	breast:
2	chr20:23336395..23338655-chr20:23399846..23402203,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269407	TF binding region
ENSG00000234832	TF binding region
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10485644	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1109557	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1122407	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12625187	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12625257	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12625297	0.80[AMR][1000 genomes]
rs12625468	0.82[AMR][1000 genomes]
rs12625489	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16985303	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16985337	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34036626	0.94[AMR][1000 genomes]
rs34831633	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736756	0.94[AMR][1000 genomes]
rs3761276	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3761278	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56693860	0.82[AMR][1000 genomes]
rs57034369	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57322153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57436024	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57535381	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58192622	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59143301	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60799291	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs61024391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61297472	0.89[AMR][1000 genomes]
rs61344818	0.94[AMR][1000 genomes]
rs7265627	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73901826	0.82[AMR][1000 genomes]
rs73901859	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73901870	0.84[AFR][1000 genomes]
rs8115832	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8117246	0.82[AMR][1000 genomes]
rs8123389	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8125332	0.82[AMR][1000 genomes]

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23332600-23337600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr20:23333000-23337800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr20:23333000-23338000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:23333000-23338000	Weak transcription	Fetal Brain Male	brain
5	chr20:23333000-23338200	Weak transcription	Brain Angular Gyrus	brain
6	chr20:23333200-23337200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:23333200-23337200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:23333200-23337600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr20:23333200-23337600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr20:23333200-23337600	Weak transcription	Stomach Mucosa	stomach
11	chr20:23333200-23337800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr20:23333200-23337800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr20:23333200-23338000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr20:23333600-23337600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr20:23333600-23337600	Strong transcription	Fetal Intestine Small	intestine
16	chr20:23333800-23337000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr20:23333800-23337000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:23333800-23337400	Genic enhancers	Dnd41	blood
19	chr20:23333800-23337400	Weak transcription	K562	blood
20	chr20:23333800-23337600	Weak transcription	Small Intestine	intestine
21	chr20:23333800-23337800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr20:23334200-23337000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr20:23334200-23337000	Strong transcription	Brain Germinal Matrix	brain
24	chr20:23334200-23337000	Strong transcription	Fetal Intestine Large	intestine
25	chr20:23334200-23337000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr20:23334200-23337000	Strong transcription	A549	lung
27	chr20:23334200-23337200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr20:23334200-23337200	Strong transcription	Fetal Thymus	thymus
29	chr20:23334400-23337000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr20:23334400-23337000	Strong transcription	Placenta	Placenta
31	chr20:23334400-23337200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr20:23334400-23337200	Strong transcription	Primary T cells from cord blood	blood
33	chr20:23334400-23337200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr20:23334600-23337000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr20:23334600-23337000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:23334600-23337000	Strong transcription	Brain Hippocampus Middle	brain
37	chr20:23334600-23337000	Strong transcription	Esophagus	oesophagus
38	chr20:23334600-23337000	Strong transcription	Gastric	stomach
39	chr20:23334600-23337200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr20:23334600-23337200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr20:23334600-23337200	Strong transcription	Fetal Brain Female	brain
42	chr20:23334600-23337400	Strong transcription	Lung	lung
43	chr20:23334600-23337600	Strong transcription	Fetal Stomach	stomach
44	chr20:23334800-23337000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr20:23335000-23337800	Weak transcription	HSMMtube	muscle
46	chr20:23335200-23338000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr20:23335600-23337600	Weak transcription	Primary B cells from cord blood	blood
48	chr20:23335600-23337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr20:23335600-23337800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr20:23335600-23337800	Weak transcription	NHEK	skin

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