Variant report

Variant	rs1053598
Chromosome Location	chr6:24704538-24704539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 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	chr6:24701280-24704812	MCF-7	breast:	n/a	n/a
5	POLR2A	chr6:24702160-24705196	K562	blood:	n/a	n/a
6	POLR2A	chr6:24701500-24704616	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:24702514-24705122	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:24701607-24706158	K562	blood:	n/a	n/a
9	CEBPB	chr6:24704365-24704616	HepG2	liver:	n/a	chr6:24704507-24704518
10	POLR2A	chr6:24702034-24704767	K562	blood:	n/a	n/a
11	POLR2A	chr6:24701665-24706460	K562	blood:	n/a	n/a
12	POLR2A	chr6:24701597-24706180	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:24701240-24704911	SK-N-MC	brain:	n/a	n/a
14	HEY1	chr6:24704430-24705121	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:24704406-24704830	GM12892	blood:	n/a	n/a
16	POLR2A	chr6:24699666-24722345	K562	blood:	n/a	n/a
17	POLR2A	chr6:24702044-24704862	GM12892	blood:	n/a	n/a
18	CCNT2	chr6:24704350-24704790	K562	blood:	n/a	n/a
19	POLR2A	chr6:24701463-24705112	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:24704191-24704594	U87	brain:	n/a	n/a
21	POLR2A	chr6:24700942-24707949	HepG2	liver:	n/a	n/a
22	CEBPB	chr6:24704345-24704678	K562	blood:	n/a	chr6:24704507-24704518
23	POLR2A	chr6:24701386-24705121	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:24701748-24704961	K562	blood:	n/a	n/a
25	POLR2A	chr6:24701617-24704820	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr6:24702324-24704951	K562	blood:	n/a	n/a
27	POLR2A	chr6:24702081-24704769	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:24704513-24704942	Hela-S3	cervix:	n/a	n/a
29	JUN	chr6:24704225-24704826	K562	blood:	n/a	n/a
30	POLR2A	chr6:24702022-24704904	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr6:24701284-24706680	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr6:24704221-24704546	ProgFib	skin:	n/a	n/a
33	POLR2A	chr6:24704508-24705002	GM12892	blood:	n/a	n/a
34	POLR2A	chr6:24702046-24705135	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:24701390-24705126	A549	lung:	n/a	n/a
36	POLR2A	chr6:24701377-24706586	GM12891	blood:	n/a	n/a
37	POLR2A	chr6:24701977-24704797	GM18505	blood:	n/a	n/a
38	POLR2A	chr6:24701216-24704724	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr6:24703784-24705063	GM12892	blood:	n/a	n/a
40	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	chr6:24666151..24668094-chr6:24703496..24705000,2	K562	blood:
5	chr6:24698262..24699902-chr6:24702109..24705579,3	MCF-7	breast:
6	chr6:24704323..24706405-chr6:24780403..24782969,2	K562	blood:

No data

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

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10946719	0.90[EUR][1000 genomes]
rs1885208	0.83[EUR][1000 genomes]
rs2092404	0.87[EUR][1000 genomes]
rs2143339	0.87[GIH][hapmap]
rs2294686	1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3777664	0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs4712839	0.82[EUR][1000 genomes]
rs4712840	0.86[EUR][1000 genomes]
rs6931502	0.82[EUR][1000 genomes]
rs6933328	0.84[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs7764633	0.81[EUR][1000 genomes]
rs7770027	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1053598	HIST1H3G	cis	cerebellum	SCAN
rs1053598	TDP2	cis	Esophagus Mucosa	GTEx
rs1053598	ZSCAN23	cis	cerebellum	SCAN
rs1053598	MRS2	cis	parietal	SCAN
rs1053598	ACOT13	cis	cerebellum	SCAN

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	chr6:24696600-24710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
9	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
10	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:24698400-24706000	Weak transcription	Fetal Brain Male	brain
15	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:24698600-24715200	Weak transcription	Fetal Heart	heart
17	chr6:24698600-24716200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:24698600-24716200	Weak transcription	Right Atrium	heart
19	chr6:24699000-24716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:24699600-24712800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:24699800-24712400	Strong transcription	Dnd41	blood
23	chr6:24700000-24716800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:24700200-24705200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:24700200-24713200	Weak transcription	Stomach Mucosa	stomach
26	chr6:24700600-24712400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:24700800-24707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:24701000-24707000	Weak transcription	Gastric	stomach
29	chr6:24701000-24711400	Strong transcription	Brain Hippocampus Middle	brain
30	chr6:24701200-24710600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr6:24701200-24711400	Strong transcription	Liver	Liver
32	chr6:24701200-24712200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:24701200-24713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:24701200-24714200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:24701400-24711000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:24701400-24711400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:24701400-24712200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:24701400-24713000	Strong transcription	Primary B cells from cord blood	blood
39	chr6:24701400-24713000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr6:24701400-24713200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:24701400-24713200	Strong transcription	Fetal Intestine Large	intestine
42	chr6:24701400-24715400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr6:24701400-24716800	Strong transcription	Placenta	Placenta
44	chr6:24701600-24712000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:24701600-24712400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr6:24701600-24714800	Strong transcription	HUVEC	blood vessel
47	chr6:24701600-24716200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr6:24701600-24716200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr6:24701600-24716200	Strong transcription	HMEC	breast
50	chr6:24701600-24716600	Strong transcription	Fetal Muscle Trunk	muscle

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