Variant report

Variant	rs719667
Chromosome Location	chr2:113342682-113342683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:133)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:133 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr2:113341389-113342697	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:113341035-113342697	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:113341634-113342706	GM15510	blood:	n/a	n/a
4	POLR2A	chr2:113341428-113342877	Hela-S3	cervix:	n/a	n/a
5	MTA3	chr2:113341029-113342926	GM12878	blood:	n/a	n/a
6	MXI1	chr2:113341045-113342848	HepG2	liver:	n/a	chr2:113342149-113342164
7	POLR2A	chr2:113341022-113342876	U87	brain:	n/a	n/a
8	SIX5	chr2:113341590-113342762	A549	lung:	n/a	n/a
9	MAX	chr2:113341452-113342712	A549	lung:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
10	POLR2A	chr2:113340936-113342770	MCF-7	breast:	n/a	n/a
11	POLR2A	chr2:113341403-113342724	U87	brain:	n/a	n/a
12	TEAD4	chr2:113341609-113342707	K562	blood:	n/a	n/a
13	POLR2A	chr2:113341582-113343043	PFSK-1	brain:	n/a	n/a
14	MYBL2	chr2:113340800-113343015	HepG2	liver:	n/a	n/a
15	FOSL2	chr2:113341624-113342821	HepG2	liver:	n/a	n/a
16	POLR2A	chr2:113341219-113342864	K562	blood:	n/a	n/a
17	TAF1	chr2:113341494-113342709	MCF-7	breast:	n/a	n/a
18	POLR2A	chr2:113341474-113342695	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:113340882-113342926	GM12878	blood:	n/a	n/a
20	GABPA	chr2:113341556-113342714	SK-N-SH	brain:	n/a	n/a
21	WRNIP1	chr2:113341166-113342855	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:113341563-113342707	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:113341551-113342773	HUVEC	blood vessel:	n/a	n/a
24	TBP	chr2:113341046-113342707	HepG2	liver:	n/a	n/a
25	NRF1	chr2:113341287-113342709	SK-N-SH	brain:	n/a	n/a
26	RELA	chr2:113341727-113342708	GM18951	blood:	n/a	n/a
27	POLR2A	chr2:113340968-113342871	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr2:113341030-113342690	K562	blood:	n/a	n/a
29	MAX	chr2:113341585-113342689	ECC-1	luminal epithelium:	n/a	chr2:113342155-113342164 chr2:113342399-113342409
30	POLR2A	chr2:113341199-113342955	PFSK-1	brain:	n/a	n/a
31	POLR2A	chr2:113340889-113342907	K562	blood:	n/a	n/a
32	TEAD4	chr2:113340959-113342912	HepG2	liver:	n/a	n/a
33	ZNF143	chr2:113341534-113342727	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF1	chr2:113341595-113342683	H1-hESC	embryonic stem cell:	n/a	n/a
35	FOXM1	chr2:113341574-113342755	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:113341020-113342850	HepG2	liver:	n/a	n/a
37	POLR2A	chr2:113341661-113342758	ECC-1	luminal epithelium:	n/a	n/a
38	REST	chr2:113341451-113342695	HepG2	liver:	n/a	n/a
39	REST	chr2:113341403-113342682	A549	lung:	n/a	n/a
40	TBP	chr2:113341529-113342700	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr2:113340958-113343554	HepG2	liver:	n/a	n/a
42	POLR2A	chr2:113341475-113342755	GM12878	blood:	n/a	n/a
43	POLR2A	chr2:113341288-113342981	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr2:113340641-113343217	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:113340694-113342890	HepG2	liver:	n/a	n/a
46	POLR2A	chr2:113341627-113342709	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:113341556-113342695	GM19099	blood:	n/a	n/a
48	ELF1	chr2:113341368-113342792	HCT-116	colon:	n/a	chr2:113341940-113341953 chr2:113341971-113341984
49	RELA	chr2:113341105-113342841	GM18505	blood:	n/a	n/a
50	POLR2A	chr2:113341078-113342689	HCT-116	colon:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99078212..99079127-chr2:113342181..113342990,2	Hela-S3	cervix:
2	chr2:113342174..113343883-chr2:113403461..113405044,2	K562	blood:
3	chr10:75006774..75007379-chr2:113341862..113342735,2	Hela-S3	cervix:
4	chr2:39351098..39351964-chr2:113341975..113342944,2	NB4	blood:
5	chr2:113335699..113339674-chr2:113340106..113343204,5	K562	blood:
6	chr2:113298954..113302477-chr2:113339455..113343767,5	MCF-7	breast:
7	chr2:113342510..113344437-chr2:113651250..113653348,2	MCF-7	breast:
8	chr2:113296892..113302637-chr2:113340004..113344909,8	K562	blood:
9	chr2:113340008..113343992-chr2:113483304..113487579,6	K562	blood:
10	chr2:113031869..113034952-chr2:113341167..113343629,3	MCF-7	breast:
11	chr2:113340774..113345524-chr2:113480391..113485957,9	MCF-7	breast:
12	chr2:113339547..113343883-chr2:113402286..113405078,6	K562	blood:
13	chr2:113237331..113240789-chr2:113339342..113343125,4	K562	blood:
14	chr2:113340479..113344233-chr2:113401874..113407323,6	MCF-7	breast:
15	chr2:113338959..113342918-chr2:113483353..113487579,5	K562	blood:
16	chr2:113298569..113302646-chr2:113339335..113343133,7	K562	blood:
17	chr17:2303358..2303980-chr2:113342107..113342737,2	Hela-S3	cervix:
18	chr2:113340437..113343949-chr2:113401268..113406617,9	MCF-7	breast:
19	chr2:113298759..113301838-chr2:113339526..113343252,4	MCF-7	breast:
20	chr2:113235824..113243298-chr2:113338675..113344022,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243389	TF binding region
ENSG00000115904	Chromatin interaction
ENSG00000070444	Chromatin interaction
ENSG00000125630	Chromatin interaction
ENSG00000144130	Chromatin interaction
ENSG00000207383	Chromatin interaction
ENSG00000165879	Chromatin interaction
ENSG00000114999	Chromatin interaction
ENSG00000236756	Chromatin interaction
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction
ENSG00000188177	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11687159	0.88[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12618629	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35832933	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3748024	0.87[CHD][hapmap];0.87[JPT][hapmap];0.92[LWK][hapmap];0.83[ASN][1000 genomes]
rs3789722	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs719668	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs719667	POLR1B	cis	parietal	SCAN
rs719667	POLR1B	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113340800-113342800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:113340800-113342800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:113340800-113343000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:113341000-113342800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr2:113341000-113342800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:113341000-113343000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:113341000-113343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:113341200-113342800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr2:113341200-113342800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr2:113341200-113342800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:113341200-113343000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:113341200-113343000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr2:113341200-113343200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:113341200-113343400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr2:113341400-113342800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr2:113341400-113342800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113341400-113342800	Active TSS	Aorta	Aorta
18	chr2:113341400-113342800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:113341400-113342800	Active TSS	Ovary	ovary
20	chr2:113341400-113342800	Active TSS	Placenta Amnion	Placenta Amnion
21	chr2:113341400-113342800	Active TSS	A549	lung
22	chr2:113341400-113343000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr2:113341400-113343000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr2:113341400-113343000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr2:113341400-113343000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:113341600-113342800	Active TSS	GM12878-XiMat	blood
27	chr2:113341600-113342800	Active TSS	Hela-S3	cervix
28	chr2:113341600-113343400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:113342200-113342800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:113342200-113343000	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr2:113342200-113343000	Flanking Active TSS	Fetal Thymus	thymus
32	chr2:113342200-113343200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr2:113342200-113343400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr2:113342400-113342800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:113342400-113342800	Flanking Active TSS	Placenta	Placenta
36	chr2:113342400-113343000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
37	chr2:113342400-113343000	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr2:113342400-113343000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr2:113342400-113343000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr2:113342400-113343000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:113342400-113343000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr2:113342400-113343000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr2:113342400-113343000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr2:113342400-113343000	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr2:113342400-113343000	Flanking Active TSS	Fetal Stomach	stomach
46	chr2:113342400-113343000	Flanking Active TSS	Pancreas	Pancrea
47	chr2:113342400-113343000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr2:113342400-113343000	Flanking Active TSS	Thymus	Thymus
49	chr2:113342400-113343000	Flanking Active TSS	HSMMtube	muscle
50	chr2:113342400-113343000	Flanking Active TSS	HUVEC	blood vessel

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