Variant report

Variant	rs6804726
Chromosome Location	chr3:112709589-112709590
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:378)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:378 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MBD4	chr3:112709307-112710245	HepG2	liver:	n/a	n/a
2	ZNF217	chr3:112709379-112710315	MCF-7	breast:	n/a	n/a
3	KAP1	chr3:112709366-112710536	HEK293	kidney:	n/a	n/a
4	CHD1	chr3:112709443-112710748	GM12878	blood:	n/a	chr3:112709691-112709701
5	POLR2A	chr3:112709428-112710398	HepG2	liver:	n/a	n/a
6	MXI1	chr3:112709359-112710470	GM12878	blood:	n/a	n/a
7	E2F6	chr3:112709485-112709888	K562	blood:	n/a	chr3:112709691-112709702
8	POLR2A	chr3:112709550-112710328	GM12891	blood:	n/a	n/a
9	CTCF	chr3:112709580-112709730	NHLF	lung:	n/a	n/a
10	MAX	chr3:112709326-112710363	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr3:112709522-112710257	K562	blood:	n/a	n/a
12	POLR2A	chr3:112709524-112710283	SK-N-SH	brain:	n/a	n/a
13	CREB1	chr3:112709513-112710509	H1-hESC	embryonic stem cell:	n/a	n/a
14	TBP	chr3:112709501-112710314	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:112709441-112710402	H1-hESC	embryonic stem cell:	n/a	n/a
16	ARID3A	chr3:112709542-112710316	HepG2	liver:	n/a	n/a
17	GABPA	chr3:112709364-112710487	A549	lung:	n/a	chr3:112709785-112709796
18	USF2	chr3:112709505-112709800	GM12878	blood:	n/a	chr3:112709558-112709569
19	HEY1	chr3:112709461-112710382	K562	blood:	n/a	n/a
20	PBX3	chr3:112709199-112710282	A549	lung:	n/a	n/a
21	MXI1	chr3:112709337-112710650	IMR90	lung:	n/a	n/a
22	CREB1	chr3:112709482-112710462	HepG2	liver:	n/a	n/a
23	NRF1	chr3:112709193-112710633	SK-N-SH	brain:	n/a	chr3:112709785-112709796 chr3:112709785-112709796
24	POLR2A	chr3:112709412-112710499	PANC-1	pancreas:	n/a	n/a
25	BCL3	chr3:112709303-112710379	A549	lung:	n/a	chr3:112709664-112709677
26	POLR2A	chr3:112709556-112710273	H1-hESC	embryonic stem cell:	n/a	n/a
27	E2F6	chr3:112709272-112710407	H1-hESC	embryonic stem cell:	n/a	chr3:112709691-112709702
28	PML	chr3:112709267-112710614	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:112709430-112710415	K562	blood:	n/a	n/a
30	EGR1	chr3:112709503-112709826	K562	blood:	n/a	chr3:112709786-112709795 chr3:112709785-112709794 chr3:112709747-112709771
31	BRCA1	chr3:112709305-112710939	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:112709430-112710345	PANC-1	pancreas:	n/a	n/a
33	RUNX3	chr3:112709411-112710525	GM12878	blood:	n/a	chr3:112710265-112710274 chr3:112710265-112710274
34	IRF1	chr3:112709416-112710392	K562	blood:	n/a	n/a
35	TEAD4	chr3:112709313-112709766	H1-hESC	embryonic stem cell:	n/a	n/a
36	GABPA	chr3:112709415-112710327	A549	lung:	n/a	chr3:112709785-112709796
37	POLR2A	chr3:112709476-112710379	ECC-1	luminal epithelium:	n/a	n/a
38	MXI1	chr3:112709544-112710620	Hela-S3	cervix:	n/a	n/a
39	MAX	chr3:112709376-112710376	NB4	blood:	n/a	n/a
40	MAX	chr3:112709189-112710548	A549	lung:	n/a	n/a
41	MAX	chr3:112709378-112710407	MCF-7	breast:	n/a	n/a
42	ZEB1	chr3:112709529-112710497	GM12878	blood:	n/a	chr3:112710041-112710050
43	POLR2A	chr3:112709393-112710426	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:112709408-112710372	U87	brain:	n/a	n/a
45	MAX	chr3:112709342-112710356	SK-N-SH	brain:	n/a	n/a
46	ZEB1	chr3:112709355-112710586	HepG2	liver:	n/a	chr3:112710041-112710050
47	ATF1	chr3:112709573-112710337	K562	blood:	n/a	n/a
48	BACH1	chr3:112709514-112710399	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr3:112709442-112710559	HepG2	liver:	n/a	n/a
50	HDAC2	chr3:112709462-112710374	MCF-7	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:
2	chr3:112709241..112710011-chr3:112737824..112738662,2	HCT-116	colon:
3	chr3:112709522..112710041-chrX:123093603..123094458,2	Hela-S3	cervix:
4	chr11:66383997..66384601-chr3:112709418..112710134,2	Hela-S3	cervix:
5	chr3:112708559..112710573-chr3:112736590..112739999,3	K562	blood:
6	chr3:112354988..112357166-chr3:112709171..112711334,2	MCF-7	breast:
7	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
8	chr1:156023107..156023865-chr3:112709415..112710123,2	Hela-S3	cervix:
9	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
10	chr3:112709111..112712767-chr3:112725826..112728376,3	K562	blood:
11	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
12	chr3:112708671..112711453-chr3:112735992..112738475,2	K562	blood:
13	chr3:112708547..112711309-chr3:112736671..112738787,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf17-2	chr3:112709294-112710000	ENSG00000272844.1

No data

Variant related genes	Relation type
GTPBP8	TF binding region
ENSG00000101972	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000240057	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000248643	Chromatin interaction
ENSG00000163608	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs57329048	1.00[AMR][1000 genomes]
rs57703274	1.00[AMR][1000 genomes]
rs57958286	1.00[AMR][1000 genomes]
rs58388252	1.00[AMR][1000 genomes]
rs59597612	1.00[AMR][1000 genomes]
rs59599263	1.00[AMR][1000 genomes]
rs60515525	1.00[AMR][1000 genomes]
rs60691321	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61078134	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61183543	1.00[AMR][1000 genomes]
rs61298854	1.00[AMR][1000 genomes]
rs6784463	1.00[AMR][1000 genomes]
rs6788565	1.00[AMR][1000 genomes]
rs73853713	1.00[AMR][1000 genomes]
rs73853715	1.00[AMR][1000 genomes]
rs73854002	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857306	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857313	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857314	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857323	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857324	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73857325	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7630531	0.92[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7643297	1.00[AMR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6804726	DOK2	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112709000-112709600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:112709000-112710000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:112709000-112710800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:112709000-112711200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:112709000-112711600	Active TSS	K562	blood
6	chr3:112709200-112709600	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr3:112709200-112709600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr3:112709200-112709600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:112709200-112709600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:112709200-112709600	Flanking Active TSS	Brain Cingulate Gyrus	brain
11	chr3:112709200-112709600	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr3:112709200-112709600	Flanking Active TSS	Hela-S3	cervix
13	chr3:112709200-112709600	Flanking Active TSS	HMEC	breast
14	chr3:112709200-112709600	Flanking Active TSS	NHEK	skin
15	chr3:112709200-112709600	Flanking Active TSS	Osteobl	bone
16	chr3:112709200-112709800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:112709200-112709800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr3:112709200-112709800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr3:112709200-112709800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:112709200-112709800	Active TSS	Brain Germinal Matrix	brain
21	chr3:112709200-112709800	Flanking Active TSS	Dnd41	blood
22	chr3:112709200-112709800	Flanking Active TSS	GM12878-XiMat	blood
23	chr3:112709200-112709800	Flanking Active TSS	HepG2	liver
24	chr3:112709200-112709800	Flanking Active TSS	HUVEC	blood vessel
25	chr3:112709200-112709800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:112709200-112710000	Active TSS	Fetal Brain Female	brain
27	chr3:112709200-112710400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:112709200-112710400	Active TSS	Adipose Nuclei	Adipose
29	chr3:112709200-112710400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr3:112709200-112710400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:112709200-112710600	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr3:112709200-112710600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:112709200-112710600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:112709200-112710600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:112709200-112710600	Active TSS	Liver	Liver
36	chr3:112709200-112710600	Active TSS	Brain Hippocampus Middle	brain
37	chr3:112709200-112710600	Active TSS	Brain Substantia Nigra	brain
38	chr3:112709200-112710600	Active TSS	Fetal Brain Male	brain
39	chr3:112709200-112710600	Active TSS	Rectal Smooth Muscle	rectum
40	chr3:112709200-112710600	Active TSS	NH-A	brain
41	chr3:112709200-112710800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr3:112709200-112710800	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr3:112709200-112710800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr3:112709200-112710800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:112709200-112710800	Active TSS	Duodenum Mucosa	Duodenum
46	chr3:112709200-112710800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:112709200-112710800	Active TSS	Fetal Heart	heart
48	chr3:112709200-112710800	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr3:112709200-112710800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:112709200-112711000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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