Variant report

Variant	rs62400787
Chromosome Location	chr6:24704017-24704018
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:24703935-24704997	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:24700987-24706658	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:24701450-24705152	K562	blood:	n/a	n/a
4	POLR2A	chr6:24701622-24704492	HCT-116	colon:	n/a	n/a
5	POLR2A	chr6:24701280-24704812	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:24703549-24704166	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:24702160-24705196	K562	blood:	n/a	n/a
8	POLR2A	chr6:24701500-24704616	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr6:24702514-24705122	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:24701607-24706158	K562	blood:	n/a	n/a
11	POLR2A	chr6:24702034-24704767	K562	blood:	n/a	n/a
12	IRF1	chr6:24703941-24704330	K562	blood:	n/a	n/a
13	POLR2A	chr6:24701665-24706460	K562	blood:	n/a	n/a
14	POLR2A	chr6:24703858-24704071	U87	brain:	n/a	n/a
15	POLR2A	chr6:24703531-24704073	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr6:24701597-24706180	HepG2	liver:	n/a	n/a
17	POLR2A	chr6:24701240-24704911	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr6:24703486-24704137	HCT-116	colon:	n/a	n/a
19	POLR2A	chr6:24699666-24722345	K562	blood:	n/a	n/a
20	POLR2A	chr6:24702044-24704862	GM12892	blood:	n/a	n/a
21	POLR2A	chr6:24703823-24704106	K562	blood:	n/a	n/a
22	MTA3	chr6:24703920-24704395	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:24701463-24705112	HepG2	liver:	n/a	n/a
24	POLR2A	chr6:24702032-24704342	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr6:24702903-24704265	GM12891	blood:	n/a	n/a
26	POLR2A	chr6:24700942-24707949	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:24701386-24705121	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:24703526-24704151	U87	brain:	n/a	n/a
29	POLR2A	chr6:24701748-24704961	K562	blood:	n/a	n/a
30	POLR2A	chr6:24701617-24704820	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr6:24702324-24704951	K562	blood:	n/a	n/a
32	POLR2A	chr6:24702081-24704769	GM12891	blood:	n/a	n/a
33	POLR2A	chr6:24703780-24704131	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:24702022-24704904	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr6:24701284-24706680	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:24703785-24704244	GM12891	blood:	n/a	n/a
37	POLR2A	chr6:24702046-24705135	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:24701390-24705126	A549	lung:	n/a	n/a
39	POLR2A	chr6:24701377-24706586	GM12891	blood:	n/a	n/a
40	POLR2A	chr6:24703829-24704071	U87	brain:	n/a	n/a
41	POLR2A	chr6:24702845-24704078	K562	blood:	n/a	n/a
42	POLR2A	chr6:24703762-24704133	U87	brain:	n/a	n/a
43	POLR2A	chr6:24701977-24704797	GM18505	blood:	n/a	n/a
44	POLR2A	chr6:24703881-24704130	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr6:24701216-24704724	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr6:24703784-24705063	GM12892	blood:	n/a	n/a
47	POLR2A	chr6:24702034-24704205	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr6:24703719-24706512	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
2	chr6:24703121..24705782-chr6:24707406..24711144,3	MCF-7	breast:
3	chr6:24666486..24669007-chr6:24703954..24705943,2	MCF-7	breast:
4	chr6:24530783..24533712-chr6:24700418..24704307,3	MCF-7	breast:
5	chr6:24666151..24668094-chr6:24703496..24705000,2	K562	blood:
6	chr6:24698262..24699902-chr6:24702109..24705579,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272402	TF binding region
ENSG00000272345	TF binding region
ENSG00000112294	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11559067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16889567	1.00[ASN][1000 genomes]
rs17243136	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17243276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17412874	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17419844	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491730	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212238	1.00[ASN][1000 genomes]
rs62400556	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62400558	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62400559	1.00[ASN][1000 genomes]
rs62400760	1.00[ASN][1000 genomes]
rs62400773	1.00[ASN][1000 genomes]
rs62400774	1.00[ASN][1000 genomes]
rs62400783	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400789	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400790	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400791	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62400792	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400793	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400795	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400819	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62400821	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62400822	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62402860	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62402864	1.00[AFR][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	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24680000-24705400	Weak transcription	Colonic Mucosa	Colon
2	chr6:24681200-24705600	Weak transcription	Ovary	ovary
3	chr6:24684800-24705400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:24684800-24705600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:24684800-24709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:24693600-24705200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr6:24696600-24704200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:24696600-24710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
10	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
11	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr6:24698400-24706000	Weak transcription	Fetal Brain Male	brain
16	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:24698600-24715200	Weak transcription	Fetal Heart	heart
18	chr6:24698600-24716200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr6:24698600-24716200	Weak transcription	Right Atrium	heart
20	chr6:24699000-24716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:24699600-24712800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr6:24699800-24712400	Strong transcription	Dnd41	blood
24	chr6:24700000-24716800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:24700200-24705200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:24700200-24713200	Weak transcription	Stomach Mucosa	stomach
27	chr6:24700600-24712400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:24700800-24707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:24701000-24707000	Weak transcription	Gastric	stomach
30	chr6:24701000-24711400	Strong transcription	Brain Hippocampus Middle	brain
31	chr6:24701200-24710600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr6:24701200-24711400	Strong transcription	Liver	Liver
33	chr6:24701200-24712200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:24701200-24713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:24701200-24714200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:24701400-24711000	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:24701400-24711400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:24701400-24712200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr6:24701400-24713000	Strong transcription	Primary B cells from cord blood	blood
40	chr6:24701400-24713000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr6:24701400-24713200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:24701400-24713200	Strong transcription	Fetal Intestine Large	intestine
43	chr6:24701400-24715400	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr6:24701400-24716800	Strong transcription	Placenta	Placenta
45	chr6:24701600-24712000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:24701600-24712400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:24701600-24714800	Strong transcription	HUVEC	blood vessel
48	chr6:24701600-24716200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr6:24701600-24716200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr6:24701600-24716200	Strong transcription	HMEC	breast

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