Variant report

Variant	rs7247057
Chromosome Location	chr19:36523990-36523991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr19:36523554-36524198	SH-SY5Y	brain:	n/a	chr19:36523702-36523711
2	YY1	chr19:36523612-36524078	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr19:36523822-36524067	H1-hESC	embryonic stem cell:	n/a	n/a
4	YY1	chr19:36523600-36524113	SK-N-SH_RA	brain:	n/a	chr19:36523604-36523618
5	POLR2A	chr19:36523582-36524039	Gliobla	brain:	n/a	n/a
6	POLR2A	chr19:36523422-36524305	U87	brain:	n/a	n/a
7	POLR2A	chr19:36523597-36524133	ProgFib	skin:	n/a	n/a
8	YY1	chr19:36523586-36524093	H1-hESC	embryonic stem cell:	n/a	chr19:36523604-36523618
9	CTCF	chr19:36523840-36523990	HFF-Myc	foreskin:	n/a	n/a
10	ZNF263	chr19:36523671-36524206	HEK293-T-REx	kidney:	n/a	n/a
11	POLR2A	chr19:36523305-36524172	H1-neurons	neurons:	n/a	n/a
12	CTCF	chr19:36523940-36524090	GM12867	blood:	n/a	n/a
13	POLR2A	chr19:36523459-36524161	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr19:36523481-36524207	PFSK-1	brain:	n/a	n/a
15	REST	chr19:36522810-36524431	H1-neurons	neurons:	n/a	chr19:36523635-36523642 chr19:36523011-36523029 chr19:36523488-36523501 chr19:36523770-36523783
16	TAF1	chr19:36523257-36524209	H1-neurons	neurons:	n/a	n/a
17	POLR2A	chr19:36523709-36524350	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:36523840-36523990	HFF	foreskin:	n/a	n/a
19	POLR2A	chr19:36523612-36524040	SK-N-SH	brain:	n/a	n/a
20	RAD21	chr19:36523770-36524001	IMR90	lung:	n/a	n/a
21	POLR2A	chr19:36523277-36524115	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr19:36523447-36524059	HUVEC	blood vessel:	n/a	n/a
23	NRF1	chr19:36523627-36523992	H1-hESC	embryonic stem cell:	n/a	chr19:36523789-36523800 chr19:36523786-36523800 chr19:36523789-36523798 chr19:36523791-36523800
24	POLR2A	chr19:36523642-36524188	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAZ	chr19:36522691-36524331	IMR90	lung:	n/a	chr19:36523773-36523783 chr19:36524013-36524022
26	POLR2A	chr19:36523555-36524302	U87	brain:	n/a	n/a
27	NRF1	chr19:36523383-36524190	SK-N-SH	brain:	n/a	chr19:36523789-36523800 chr19:36523786-36523800 chr19:36523789-36523798 chr19:36523791-36523800
28	TAF1	chr19:36523569-36524083	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr19:36523555-36524284	U87	brain:	n/a	n/a
30	POLR2A	chr19:36523591-36524123	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr19:36523428-36524285	U87	brain:	n/a	n/a
32	POLR2A	chr19:36523400-36524254	SK-N-MC	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:36523945-36523995	HEK293	kidney:	embryo
2	chr19:36523945-36523995	NHDF-neo	bronchial:	n/a
3	chr19:36523945-36523995	BE2_C	brain:	n/a
4	chr19:36523945-36523995	AoSMC	blood vessel:	n/a
5	chr19:36523945-36523995	Hela-S3	cervix:	n/a
6	chr19:36523945-36523995	MCF10A-Er-Src	breast:	n/a
7	chr19:36523945-36523995	SK-N-SH_RA	brain:	n/a
8	chr19:36523945-36523995	NHBE	bronchial:	n/a
9	chr19:36523945-36523995	AG04449	skin:	fetal
10	chr19:36523945-36523995	GM12878	blood:	n/a
11	chr19:36523945-36523995	HCPEpiC	choroid plexus:	n/a
12	chr19:36523945-36523995	T-47D	breast:	n/a
13	chr19:36523945-36523995	HRCEpiC	kidney:	n/a
14	chr19:36523945-36523995	GM19239	blood:	n/a
15	chr19:36523945-36523995	ECC-1	luminal epithelium:	n/a
16	chr19:36523945-36523995	GM06990	blood:	n/a
17	chr19:36523945-36523995	AG04450	lung:	fetal
18	chr19:36523945-36523995	NB4	blood:	n/a
19	chr19:36523945-36523995	Hepatocyte	liver:	n/a
20	chr19:36523945-36523995	HPAEpiC	pulmonary alveolar:	n/a
21	chr19:36523945-36523995	BJ	skin:	n/a
22	chr19:36523945-36523995	LNCaP	prostate:	n/a
23	chr19:36523945-36523995	AG09319	gingival:	n/a
24	chr19:36523945-36523995	A549	lung:	n/a
25	chr19:36523945-36523995	HCF	heart:	n/a
26	chr19:36523945-36523995	HUVEC	blood vessel:	n/a
27	chr19:36523945-36523995	HNPCEpiC	eye:	n/a
28	chr19:36523945-36523995	PrEC	prostate:	n/a
29	chr19:36523945-36523995	K562	blood:	n/a
30	chr19:36523945-36523995	HCT-116	colon:	n/a
31	chr19:36523945-36523995	HepG2	liver:	n/a
32	chr19:36523945-36523995	GM12891	blood:	n/a
33	chr19:36523945-36523995	SK-N-MC	brain:	n/a
34	chr19:36523945-36523995	U87	brain:	n/a
35	chr19:36523945-36523995	PFSK-1	brain:	n/a
36	chr19:36523945-36523995	ovcar-3	ovarian:	n/a
37	chr19:36523945-36523995	NH-A	brain:	n/a
38	chr19:36523945-36523995	HCM	heart:	n/a
39	chr19:36523945-36523995	IMR90	lung:	fetal
40	chr19:36523945-36523995	PANC-1	pancreas:	n/a
41	chr19:36523945-36523995	HMEC	breast:	n/a
42	chr19:36523945-36523995	GM12892	blood:	n/a
43	chr19:36523945-36523995	RPTEC	kidney:	n/a
44	chr19:36523945-36523995	AG10803	skin:	n/a
45	chr19:36523945-36523995	HRPEpiC	eye:	n/a
46	chr19:36523945-36523995	SK-N-SH	brain:	n/a
47	chr19:36523945-36523995	Jurkat	blood:	n/a
48	chr19:36523945-36523995	HEEpiC	esophagus:	n/a
49	chr19:36523945-36523995	H1-hESC	embryonic stem cell:	embryo
50	chr19:36523945-36523995	HIPEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36512890..36520143-chr19:36521963..36527491,9	K562	blood:

No data

Variant related genes	Relation type
CLIP3	TF binding region
CLIP3	CpG island
ENSG00000105270	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10418015	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420353	0.88[JPT][hapmap]
rs10421966	0.90[JPT][hapmap]
rs10426582	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs12976812	0.95[JPT][hapmap]
rs12979093	0.84[EUR][1000 genomes]
rs12981654	0.91[JPT][hapmap]
rs34906485	0.81[EUR][1000 genomes]
rs3810445	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs4805154	0.91[JPT][hapmap]
rs4805155	0.84[EUR][1000 genomes]
rs4806252	0.85[EUR][1000 genomes]
rs4806253	0.85[EUR][1000 genomes]
rs56034793	0.83[EUR][1000 genomes]
rs62109743	0.83[EUR][1000 genomes]
rs7245762	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7250448	0.86[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs7257383	0.85[TSI][hapmap];0.81[EUR][1000 genomes]

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	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7247057	PSG2	cis	parietal	SCAN
rs7247057	PSG9	cis	cerebellum	SCAN
rs7247057	ACTN4	cis	cerebellum	SCAN
rs7247057	PHLDB3	cis	parietal	SCAN
rs7247057	CYP2A7	cis	parietal	SCAN
rs7247057	POLR2I	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36506800-36532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:36507000-36532200	Weak transcription	Hela-S3	cervix
4	chr19:36508800-36532400	Weak transcription	NHEK	skin
5	chr19:36513600-36525600	Weak transcription	K562	blood
6	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
8	chr19:36516400-36532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:36517000-36526400	Weak transcription	HepG2	liver
10	chr19:36518600-36524000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:36518800-36532200	Weak transcription	A549	lung
12	chr19:36522000-36524200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr19:36522200-36524000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:36522200-36524000	Active TSS	Fetal Kidney	kidney
15	chr19:36522200-36524200	Active TSS	Brain Cingulate Gyrus	brain
16	chr19:36522200-36524400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:36522200-36524400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:36522400-36524000	Enhancers	Liver	Liver
19	chr19:36522400-36524000	Active TSS	Brain Angular Gyrus	brain
20	chr19:36522400-36524000	Active TSS	NHLF	lung
21	chr19:36522600-36524000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr19:36522600-36524000	Active TSS	Brain Anterior Caudate	brain
23	chr19:36522800-36524000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr19:36522800-36524000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:36522800-36524000	Active TSS	Fetal Brain Female	brain
26	chr19:36522800-36524200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:36522800-36524200	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr19:36522800-36524200	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr19:36522800-36524200	Active TSS	HSMMtube	muscle
30	chr19:36522800-36524400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr19:36522800-36524400	Active TSS	Rectal Smooth Muscle	rectum
32	chr19:36523000-36524000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:36523000-36524000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:36523000-36524000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr19:36523000-36524000	Active TSS	Brain Substantia Nigra	brain
36	chr19:36523000-36524000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
37	chr19:36523000-36524000	Active TSS	Ovary	ovary
38	chr19:36523000-36524000	Active TSS	NH-A	brain
39	chr19:36523000-36524000	Active TSS	Osteobl	bone
40	chr19:36523000-36524200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:36523000-36524200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:36523000-36524200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:36523000-36524200	Active TSS	Aorta	Aorta
44	chr19:36523000-36524200	Active TSS	Colonic Mucosa	Colon
45	chr19:36523000-36524200	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr19:36523000-36524200	Flanking Active TSS	Fetal Thymus	thymus
47	chr19:36523000-36524200	Active TSS	Right Atrium	heart
48	chr19:36523000-36524200	Active TSS	HSMM	muscle
49	chr19:36523000-36524400	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr19:36523000-36524400	Active TSS	Colon Smooth Muscle	Colon

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