Variant report

Variant	rs701008
Chromosome Location	chr12:58117645-58117646
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58116587-58118899	GM19193	blood:	n/a	n/a
2	MTA3	chr12:58117182-58118459	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:58117362-58118284	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:58116495-58119415	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:58117097-58118679	HL-60	blood:	n/a	n/a
6	POLR2A	chr12:58116503-58119299	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:58116328-58119086	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:58117083-58117647	HCT-116	colon:	n/a	n/a
9	POLR2A	chr12:58116411-58117973	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr12:58117597-58117653	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr12:58117045-58119241	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:58116335-58118479	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:58117571-58118458	GM12892	blood:	n/a	n/a
14	POLR2A	chr12:58117256-58118311	HepG2	liver:	n/a	n/a
15	POLR2A	chr12:58112700-58119120	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:58117082-58117846	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr12:58117124-58118952	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:58116535-58118789	K562	blood:	n/a	n/a
19	POLR2A	chr12:58114798-58119096	K562	blood:	n/a	n/a
20	NFATC1	chr12:58117519-58118039	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:58117556-58118152	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr12:58116445-58118432	HL-60	blood:	n/a	n/a
23	POLR2A	chr12:58117104-58118084	SK-N-SH	brain:	n/a	n/a
24	NFATC1	chr12:58117287-58117798	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58002964..58008004-chr12:58117447..58122099,5	MCF-7	breast:
2	chr12:57906816..57909799-chr12:58115546..58118135,2	K562	blood:
3	chr12:58085694..58088995-chr12:58116929..58123534,7	MCF-7	breast:
4	chr12:58099859..58102384-chr12:58116011..58117778,2	MCF-7	breast:
5	chr12:58104338..58106820-chr12:58115614..58118088,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AGAP2-1	chr12:58117572-58117741	ENSG00000257499.1
2	lnc-AGAP2-1	chr12:58117544-58118237	ENSG00000257499.2
3	lnc-AGAP2-1	chr12:58117544-58117741	ENSG00000257499.2

No data

Variant related genes	Relation type
ENSG00000257342	TF binding region
AGAP2-AS1	TF binding region
ENSG00000135506	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10431552	0.81[TSI][hapmap]
rs10783847	0.81[TSI][hapmap]
rs10876993	0.82[CHD][hapmap]
rs10876994	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10877011	0.89[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.84[TSI][hapmap]
rs10877012	0.81[TSI][hapmap]
rs10877013	0.81[TSI][hapmap]
rs10877014	0.81[TSI][hapmap]
rs10877015	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs10877016	0.81[TSI][hapmap]
rs10877019	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11172333	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11172335	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11172344	0.81[TSI][hapmap]
rs11172349	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs11172351	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs1689585	0.87[CHD][hapmap]
rs1689595	0.82[CHD][hapmap]
rs1696466	0.81[ASN][1000 genomes]
rs1875124	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs2069502	0.81[GIH][hapmap]
rs2072052	0.81[GIH][hapmap]
rs2269720	0.81[JPT][hapmap]
rs238516	0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs2640629	0.87[CHD][hapmap]
rs2640631	0.87[CHD][hapmap]
rs3825079	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs4646536	0.81[TSI][hapmap]
rs4760168	0.85[CHD][hapmap]
rs6581155	0.81[TSI][hapmap]
rs701006	0.85[CHD][hapmap];0.84[GIH][hapmap]
rs703842	0.81[TSI][hapmap]
rs73123375	0.80[ASN][1000 genomes]
rs774890	0.87[CHD][hapmap]
rs7979246	0.85[CHD][hapmap]
rs8181644	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv1851618	chr12:58109302-58131947	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs701008	KIAA0748	cis	cerebellum	SCAN
rs701008	FAM119B	cis	lymphoblastoid	seeQTL
rs701008	WIBG	cis	cerebellum	SCAN
rs701008	FAM119B	cis	Cerebellum	GTEx
rs701008	CDK4	cis	cerebellum	SCAN
rs701008	GPR84	cis	cerebellum	SCAN
rs701008	HOXC5	cis	cerebellum	SCAN
rs701008	LACRT	cis	parietal	SCAN
rs701008	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs701008	METTL21B	cis	lung	GTEx
rs701008	FAM119B	cis	Lymphoblastoid	GTEx
rs701008	NCKAP1L	cis	parietal	SCAN
rs701008	TSPAN31	cis	cerebellum	SCAN
rs701008	METTL21B	cis	Esophagus Muscularis	GTEx
rs701008	FAM119B	cis	cerebellum	SCAN
rs701008	DKFZP586D0919	cis	multi-tissue	Pritchard
rs701008	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs701008	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs701008	METTL21B	cis	Whole Blood	GTEx
rs701008	KRT75	cis	cerebellum	SCAN
rs701008	ESPL1	cis	parietal	SCAN
rs701008	FAM119B	cis	brain	seeQTL
rs701008	XRCC6BP1	cis	brain	seeQTL
rs701008	METTL21B	cis	Adipose Subcutaneous	GTEx
rs701008	FAM119B	cis	parietal	SCAN
rs701008	TSFM	cis	Muscle Skeletal	GTEx
rs701008	TSPAN31	cis	parietal	SCAN
rs701008	TSFM	cis	lymphoblastoid	seeQTL
rs701008	FAM119B	cis	Frontal Cortex	GTEx
rs701008	METTL21B	cis	Esophagus Mucosa	GTEx
rs701008	KRT5	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58106200-58120000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:58110000-58119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:58112200-58119600	Weak transcription	NHDF-Ad	bronchial
5	chr12:58113400-58119600	Weak transcription	Hela-S3	cervix
6	chr12:58113400-58119600	Weak transcription	HSMM	muscle
7	chr12:58113400-58119600	Weak transcription	NHEK	skin
8	chr12:58113600-58119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:58113800-58117800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:58113800-58119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:58114000-58117800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:58114000-58120600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr12:58114200-58119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:58114400-58119000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:58114400-58119600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:58115000-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:58115000-58119800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr12:58115000-58120800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:58115200-58118000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:58115200-58118200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:58115200-58119600	Weak transcription	HUVEC	blood vessel
22	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
23	chr12:58115400-58118000	Weak transcription	Osteobl	bone
24	chr12:58115400-58119000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr12:58115400-58119600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:58115400-58119600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:58115400-58119600	Weak transcription	HepG2	liver
28	chr12:58115600-58118200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:58115600-58119000	Weak transcription	Primary B cells from cord blood	blood
30	chr12:58115600-58119200	Weak transcription	HMEC	breast
31	chr12:58115600-58119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:58115600-58119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:58115600-58119600	Weak transcription	Colonic Mucosa	Colon
34	chr12:58115600-58119800	Weak transcription	Pancreas	Pancrea
35	chr12:58115600-58124000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:58115800-58118000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:58115800-58118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:58115800-58118000	Weak transcription	Brain Hippocampus Middle	brain
39	chr12:58115800-58118400	Weak transcription	Primary T cells from cord blood	blood
40	chr12:58115800-58118800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:58115800-58118800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:58115800-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:58115800-58119600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:58115800-58119600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr12:58115800-58119600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:58115800-58119600	Weak transcription	Brain Anterior Caudate	brain
47	chr12:58115800-58119600	Weak transcription	Left Ventricle	heart
48	chr12:58115800-58119600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:58115800-58119600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr12:58115800-58119600	Weak transcription	NHLF	lung

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