Variant report

Variant	rs238516
Chromosome Location	chr12:58117355-58117356
allele	A/G
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:5)
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	chr12:58116587-58118899	GM19193	blood:	n/a	n/a
2	POLR2A	chr12:58117197-58117587	GM12892	blood:	n/a	n/a
3	ESR1	chr12:58117037-58117367	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr12:58117140-58117421	GM12878	blood:	n/a	n/a
5	ZNF217	chr12:58117117-58117424	MCF-7	breast:	n/a	n/a
6	MTA3	chr12:58117182-58118459	GM12878	blood:	n/a	n/a
7	MYC	chr12:58117233-58117387	MCF-7	breast:	n/a	n/a
8	EP300	chr12:58116993-58117435	MCF-7	breast:	n/a	chr12:58117159-58117168
9	POLR2A	chr12:58116495-58119415	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:58117339-58117425	H1-hESC	embryonic stem cell:	n/a	n/a
11	ESR1	chr12:58117070-58117401	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr12:58117073-58117460	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr12:58117097-58118679	HL-60	blood:	n/a	n/a
14	POLR2A	chr12:58116503-58119299	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:58116328-58119086	GM12878	blood:	n/a	n/a
16	MYC	chr12:58117183-58117364	MCF-7	breast:	n/a	n/a
17	POLR2A	chr12:58117083-58117647	HCT-116	colon:	n/a	n/a
18	POLR2A	chr12:58116411-58117973	SK-N-MC	brain:	n/a	n/a
19	POLR2A	chr12:58117045-58119241	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:58116335-58118479	GM12892	blood:	n/a	n/a
21	POLR2A	chr12:58117152-58117540	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:58116531-58117531	K562	blood:	n/a	n/a
23	POLR2A	chr12:58117256-58118311	HepG2	liver:	n/a	n/a
24	POLR2A	chr12:58116930-58117480	K562	blood:	n/a	n/a
25	POLR2A	chr12:58117280-58117490	MCF10A-Er-Src	breast:	n/a	n/a
26	HA-E2F1	chr12:58116744-58117499	MCF-7	breast:	n/a	chr12:58117184-58117191
27	POLR2A	chr12:58112700-58119120	GM12891	blood:	n/a	n/a
28	POLR2A	chr12:58117092-58117434	HCT-116	colon:	n/a	n/a
29	POLR2A	chr12:58117082-58117846	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr12:58117124-58118952	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:58116535-58118789	K562	blood:	n/a	n/a
32	POLR2A	chr12:58117189-58117399	A549	lung:	n/a	n/a
33	POLR2A	chr12:58114798-58119096	K562	blood:	n/a	n/a
34	POLR2A	chr12:58117192-58117382	A549	lung:	n/a	n/a
35	POLR2A	chr12:58117046-58117602	MCF-7	breast:	n/a	n/a
36	POLR2A	chr12:58116445-58118432	HL-60	blood:	n/a	n/a
37	POLR2A	chr12:58117142-58117448	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr12:58117104-58118084	SK-N-SH	brain:	n/a	n/a
39	NFATC1	chr12:58117287-58117798	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:58117086-58117461	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:58116094..58117634-chr12:58133329..58135229,2	K562	blood:
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:

No data

Variant related genes	Relation type
AGAP2-AS1	TF binding region
ENSG00000257342	TF binding region
ENSG00000166986	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000135506	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10082911	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10083154	0.82[JPT][hapmap]
rs10783842	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10783843	0.80[AMR][1000 genomes]
rs10783844	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10876993	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs10877001	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10877006	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10877007	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10877008	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10877011	0.81[GIH][hapmap]
rs11172306	0.85[AMR][1000 genomes]
rs1628552	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1633360	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1633361	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1678504	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1678505	0.81[ASN][1000 genomes]
rs1678516	0.88[JPT][hapmap]
rs1678540	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1689584	0.82[ASN][1000 genomes]
rs1689585	0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs1689586	0.81[ASN][1000 genomes]
rs1689595	0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs1696466	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619441	0.82[ASN][1000 genomes]
rs2640629	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs2640631	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs2928061	0.81[ASN][1000 genomes]
rs2928062	0.82[ASN][1000 genomes]
rs2928064	0.84[ASN][1000 genomes]
rs3825078	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4760168	0.82[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs701006	0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs701008	0.86[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.83[ASN][1000 genomes]
rs7295422	0.82[MKK][hapmap]
rs7311632	0.81[MKK][hapmap]
rs774887	0.88[JPT][hapmap]
rs774890	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs7976852	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7979246	0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs799265	0.85[YRI][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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs238516	FAM119B	cis	lymphoblastoid	seeQTL
rs238516	KRT75	cis	cerebellum	SCAN
rs238516	CDK4	cis	cerebellum	SCAN
rs238516	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs238516	TSPAN31	cis	parietal	SCAN
rs238516	FAM119B	cis	parietal	SCAN
rs238516	HSD17B6	cis	cerebellum	SCAN
rs238516	KRT5	cis	cerebellum	SCAN
rs238516	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs238516	MAP3K12	cis	parietal	SCAN
rs238516	HOXC5	cis	cerebellum	SCAN
rs238516	TSPAN31	cis	cerebellum	SCAN
rs238516	CDK2	cis	parietal	SCAN
rs238516	FAM119B	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58094400-58119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58098400-58117600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:58106200-58120000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:58110000-58119800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:58112200-58119600	Weak transcription	NHDF-Ad	bronchial
6	chr12:58113200-58117400	Weak transcription	Fetal Kidney	kidney
7	chr12:58113400-58119600	Weak transcription	Hela-S3	cervix
8	chr12:58113400-58119600	Weak transcription	HSMM	muscle
9	chr12:58113400-58119600	Weak transcription	NHEK	skin
10	chr12:58113600-58119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:58113800-58117800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:58113800-58119800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:58114000-58117800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:58114000-58120600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr12:58114200-58119600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:58114400-58119000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:58114400-58119600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:58114800-58117600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:58115000-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:58115000-58119800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:58115000-58120800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:58115200-58118000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:58115200-58118200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:58115200-58119600	Weak transcription	HUVEC	blood vessel
25	chr12:58115200-58123600	Weak transcription	GM12878-XiMat	blood
26	chr12:58115400-58118000	Weak transcription	Osteobl	bone
27	chr12:58115400-58119000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:58115400-58119600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:58115400-58119600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:58115400-58119600	Weak transcription	HepG2	liver
31	chr12:58115600-58118200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:58115600-58119000	Weak transcription	Primary B cells from cord blood	blood
33	chr12:58115600-58119200	Weak transcription	HMEC	breast
34	chr12:58115600-58119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:58115600-58119600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:58115600-58119600	Weak transcription	Colonic Mucosa	Colon
37	chr12:58115600-58119800	Weak transcription	Pancreas	Pancrea
38	chr12:58115600-58124000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:58115800-58117400	Weak transcription	Fetal Lung	lung
40	chr12:58115800-58117600	Weak transcription	Fetal Intestine Large	intestine
41	chr12:58115800-58118000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:58115800-58118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:58115800-58118000	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:58115800-58118400	Weak transcription	Primary T cells from cord blood	blood
45	chr12:58115800-58118800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:58115800-58118800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr12:58115800-58119200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:58115800-58119600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:58115800-58119600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr12:58115800-58119600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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