Variant report

Variant	rs10946719
Chromosome Location	chr6:24702964-24702965
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:61)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:61 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:24700987-24706658	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:24701450-24705152	K562	blood:	n/a	n/a
3	POLR2A	chr6:24702578-24703467	HL-60	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	chr6:24702555-24703757	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr6:24702087-24703510	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:24702160-24705196	K562	blood:	n/a	n/a
9	POLR2A	chr6:24702099-24703022	K562	blood:	n/a	n/a
10	POLR2A	chr6:24701500-24704616	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr6:24702514-24705122	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:24701607-24706158	K562	blood:	n/a	n/a
13	POLR2A	chr6:24702034-24704767	K562	blood:	n/a	n/a
14	POLR2A	chr6:24701665-24706460	K562	blood:	n/a	n/a
15	MTA3	chr6:24701937-24703627	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:24702870-24703765	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:24701597-24706180	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:24702763-24703295	U87	brain:	n/a	n/a
19	POLR2A	chr6:24701240-24704911	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr6:24702754-24703391	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:24699666-24722345	K562	blood:	n/a	n/a
22	POLR2A	chr6:24702671-24703270	U87	brain:	n/a	n/a
23	POLR2A	chr6:24702916-24703289	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr6:24702892-24703753	GM12892	blood:	n/a	n/a
25	POLR2A	chr6:24702044-24704862	GM12892	blood:	n/a	n/a
26	POLR2A	chr6:24702485-24703334	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr6:24700928-24703448	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr6:24702131-24703766	GM12892	blood:	n/a	n/a
29	POLR2A	chr6:24701463-24705112	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:24702651-24703470	U87	brain:	n/a	n/a
31	POLR2A	chr6:24702032-24704342	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:24702903-24704265	GM12891	blood:	n/a	n/a
33	POLR2A	chr6:24700942-24707949	HepG2	liver:	n/a	n/a
34	NFATC1	chr6:24702015-24703528	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:24701386-24705121	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:24701748-24704961	K562	blood:	n/a	n/a
37	POLR2A	chr6:24702068-24703771	GM12891	blood:	n/a	n/a
38	POLR2A	chr6:24701617-24704820	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr6:24702871-24703614	GM12892	blood:	n/a	n/a
40	POLR2A	chr6:24702324-24704951	K562	blood:	n/a	n/a
41	POLR2A	chr6:24702920-24703247	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr6:24702081-24704769	GM12891	blood:	n/a	n/a
43	POLR2A	chr6:24702887-24703464	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:24702022-24704904	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr6:24701284-24706680	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:24702046-24705135	GM12878	blood:	n/a	n/a
47	POLR2A	chr6:24701390-24705126	A549	lung:	n/a	n/a
48	POLR2A	chr6:24701377-24706586	GM12891	blood:	n/a	n/a
49	NFATC1	chr6:24701854-24703761	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:24702845-24704078	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:24696748..24707740-chr6:24716503..24724189,24	MCF-7	breast:
2	chr6:24530783..24533712-chr6:24700418..24704307,3	MCF-7	breast:
3	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

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1053598	0.90[EUR][1000 genomes]
rs1885208	0.88[EUR][1000 genomes]
rs1923186	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2092404	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777664	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3813685	0.91[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4712839	0.87[EUR][1000 genomes]
rs4712840	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6931502	0.87[EUR][1000 genomes]
rs6933328	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764633	0.86[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10946719	TDP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24674600-24703400	Weak transcription	Aorta	Aorta
2	chr6:24680000-24705400	Weak transcription	Colonic Mucosa	Colon
3	chr6:24681200-24705600	Weak transcription	Ovary	ovary
4	chr6:24682400-24703000	Weak transcription	Lung	lung
5	chr6:24684800-24705400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:24684800-24705600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:24684800-24709000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr6:24685800-24703600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:24686200-24703000	Weak transcription	HSMM	muscle
10	chr6:24686200-24703400	Weak transcription	Fetal Kidney	kidney
11	chr6:24687600-24703000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:24687600-24703400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:24688000-24704000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:24691000-24703200	Weak transcription	Spleen	Spleen
15	chr6:24693200-24703000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:24693600-24704000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:24693600-24705200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:24693800-24703000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr6:24696200-24703000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:24696200-24703800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr6:24696600-24704200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:24696600-24710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:24696800-24703000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:24697200-24703200	Weak transcription	NHDF-Ad	bronchial
25	chr6:24697800-24703000	Weak transcription	Small Intestine	intestine
26	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
27	chr6:24698000-24703400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
29	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:24698400-24704000	Weak transcription	Hela-S3	cervix
34	chr6:24698400-24706000	Weak transcription	Fetal Brain Male	brain
35	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:24698600-24715200	Weak transcription	Fetal Heart	heart
37	chr6:24698600-24716200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr6:24698600-24716200	Weak transcription	Right Atrium	heart
39	chr6:24699000-24716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:24699600-24712800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr6:24699800-24712400	Strong transcription	Dnd41	blood
43	chr6:24700000-24703000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:24700000-24716800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:24700200-24703000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:24700200-24703000	Weak transcription	K562	blood
47	chr6:24700200-24704000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr6:24700200-24705200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:24700200-24713200	Weak transcription	Stomach Mucosa	stomach
50	chr6:24700600-24703200	Weak transcription	Brain Angular Gyrus	brain

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