Variant report

Variant	rs3746002
Chromosome Location	chr19:44123894-44123895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr19:44123055-44124402	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:44122812-44125506	K562	blood:	n/a	n/a
3	PML	chr19:44123134-44124373	K562	blood:	n/a	n/a
4	JUND	chr19:44123584-44123950	HepG2	liver:	n/a	n/a
5	PML	chr19:44122919-44124354	K562	blood:	n/a	n/a
6	POLR2A	chr19:44122976-44124502	H1-hESC	embryonic stem cell:	n/a	n/a
7	PAX5	chr19:44123478-44124091	GM12892	blood:	n/a	n/a
8	ZBTB7A	chr19:44123443-44124363	K562	blood:	n/a	chr19:44123661-44123670
9	MAX	chr19:44122847-44124613	HepG2	liver:	n/a	n/a
10	NRF1	chr19:44122822-44124616	SK-N-SH	brain:	n/a	chr19:44123821-44123830 chr19:44124209-44124223 chr19:44123819-44123830 chr19:44124214-44124223 chr19:44123761-44123775 chr19:44124212-44124223 chr19:44123985-44123996 chr19:44124212-44124221 chr19:44124212-44124226 chr19:44124212-44124223 chr19:44123819-44123833
11	HA-E2F1	chr19:44123069-44124510	MCF-7	breast:	n/a	chr19:44123765-44123774 chr19:44124213-44124222 chr19:44123709-44123719 chr19:44123820-44123829 chr19:44123738-44123748 chr19:44123741-44123751
12	POLR2A	chr19:44122957-44125410	SK-N-MC	brain:	n/a	n/a
13	JUND	chr19:44123611-44124019	H1-hESC	embryonic stem cell:	n/a	n/a
14	GTF2F1	chr19:44123037-44124455	K562	blood:	n/a	n/a
15	YY1	chr19:44123375-44124314	GM12878	blood:	n/a	chr19:44123714-44123728 chr19:44123717-44123731
16	RELA	chr19:44123040-44124236	GM19099	blood:	n/a	n/a
17	TAF1	chr19:44122986-44124307	ECC-1	luminal epithelium:	n/a	n/a
18	FOXM1	chr19:44122977-44124446	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:44122909-44124594	K562	blood:	n/a	n/a
20	RCOR1	chr19:44123073-44123953	Hela-S3	cervix:	n/a	n/a
21	HMGN3	chr19:44123349-44124551	K562	blood:	n/a	n/a
22	TBP	chr19:44123007-44124646	K562	blood:	n/a	n/a
23	TAF1	chr19:44123564-44123932	PFSK-1	brain:	n/a	n/a
24	RCOR1	chr19:44123538-44124171	GM12878	blood:	n/a	n/a
25	REST	chr19:44122992-44124103	SK-N-SH	brain:	n/a	chr19:44123851-44123858 chr19:44123506-44123513 chr19:44124033-44124046 chr19:44123747-44123760
26	MYC	chr19:44122958-44125116	K562	blood:	n/a	n/a
27	POLR2A	chr19:44122432-44126679	HepG2	liver:	n/a	n/a
28	MAX	chr19:44123075-44124408	K562	blood:	n/a	n/a
29	E2F6	chr19:44123392-44124527	K562	blood:	n/a	chr19:44123765-44123774 chr19:44124213-44124222 chr19:44123709-44123719 chr19:44123820-44123829 chr19:44123738-44123748 chr19:44123741-44123751
30	ARID3A	chr19:44123082-44125051	K562	blood:	n/a	n/a
31	ZC3H11A	chr19:44123091-44124995	K562	blood:	n/a	n/a
32	POLR2A	chr19:44123041-44124398	U87	brain:	n/a	n/a
33	CTCF	chr19:44123081-44124467	K562	blood:	n/a	n/a
34	MAX	chr19:44123186-44124049	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr19:44122774-44124609	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr19:44122957-44124465	GM19193	blood:	n/a	n/a
37	EP300	chr19:44123656-44124213	H1-hESC	embryonic stem cell:	n/a	chr19:44123719-44123728 chr19:44123710-44123719 chr19:44123739-44123748 chr19:44123716-44123725 chr19:44124086-44124100 chr19:44123904-44123913
38	YY1	chr19:44122988-44124194	HepG2	liver:	n/a	chr19:44123714-44123728 chr19:44123717-44123731
39	POLR2A	chr19:44122935-44124698	HCT-116	colon:	n/a	n/a
40	BRCA1	chr19:44123762-44123962	HepG2	liver:	n/a	n/a
41	HEY1	chr19:44122947-44124448	HepG2	liver:	n/a	chr19:44123989-44124004 chr19:44123901-44123916 chr19:44123896-44123911
42	TAF1	chr19:44122995-44124294	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:44122919-44124681	PFSK-1	brain:	n/a	n/a
44	POLR2A	chr19:44122919-44124400	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:44122936-44125145	K562	blood:	n/a	n/a
46	POLR2A	chr19:44122989-44124466	GM12878	blood:	n/a	n/a
47	NFIC	chr19:44123226-44124168	ECC-1	luminal epithelium:	n/a	n/a
48	MAZ	chr19:44123097-44124593	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:44122920-44124527	HepG2	liver:	n/a	n/a
50	TCF7L2	chr19:44122965-44124296	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44078138..44080459-chr19:44123311..44124978,2	MCF-7	breast:
2	chr19:44097500..44104541-chr19:44116930..44130620,31	K562	blood:
3	chr19:44122624..44125256-chr19:44141958..44145749,5	MCF-7	breast:
4	chr19:44098736..44101941-chr19:44122253..44126181,8	MCF-7	breast:
5	chr19:44122279..44128380-chr19:44171168..44174381,7	K562	blood:
6	chr19:44097777..44104240-chr19:44121602..44130880,30	K562	blood:
7	chr19:44118551..44131201-chr19:44135615..44147023,20	K562	blood:
8	chr19:44077515..44081647-chr19:44122454..44125105,4	K562	blood:
9	chr19:44079594..44081331-chr19:44123672..44125242,2	MCF-7	breast:
10	chr19:44121917..44126953-chr19:44140515..44144634,11	MCF-7	breast:
11	chr19:44036740..44039638-chr19:44122133..44124023,3	MCF-7	breast:
12	chr19:44123600..44125300-chr19:44174551..44176113,2	K562	blood:
13	chr19:44122405..44124200-chr19:44172139..44174379,2	MCF-7	breast:
14	chr19:44122148..44124570-chr19:44257332..44259810,2	K562	blood:
15	chr19:44098671..44105555-chr19:44121892..44125342,15	MCF-7	breast:
16	chr19:44082516..44084852-chr19:44122314..44123953,3	K562	blood:
17	chr1:113161371..113161879-chr19:44123396..44124353,2	Hela-S3	cervix:
18	chr19:43967559..43969177-chr19:44122484..44124753,2	K562	blood:
19	chr19:44121942..44125768-chr19:44258526..44260737,4	K562	blood:
20	chr19:44121491..44126230-chr19:44171612..44176113,5	K562	blood:
21	chr19:44122865..44126194-chr19:44171417..44174035,3	MCF-7	breast:
22	chr19:44036629..44040127-chr19:44122528..44124622,4	K562	blood:

Variant related genes	Relation type
ZNF428	TF binding region
ENSG00000011422	Chromatin interaction
ENSG00000269583	Chromatin interaction
ENSG00000124466	Chromatin interaction
ENSG00000073050	Chromatin interaction
ENSG00000226763	Chromatin interaction
ENSG00000234465	Chromatin interaction
ENSG00000105767	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000105771	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000167378	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11083712	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671645	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12461175	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1402325	0.85[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1402326	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17655574	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs1879387	0.94[EUR][1000 genomes]
rs2003098	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2079646	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2302421	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3746003	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3815422	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803643	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4803644	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73038867	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs767540	0.85[CEU][hapmap];0.84[GIH][hapmap];0.82[EUR][1000 genomes]
rs880108	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3746002	PRRG2	cis	cerebellum	SCAN
rs3746002	IZUMO2	cis	parietal	SCAN
rs3746002	MED25	cis	cerebellum	SCAN
rs3746002	ZNF480	cis	parietal	SCAN
rs3746002	VSIG10L	cis	parietal	SCAN
rs3746002	ZNF615	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44122400-44124200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:44122400-44124400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:44122600-44124200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:44122600-44124200	Active TSS	A549	lung
5	chr19:44122600-44124200	Active TSS	HSMMtube	muscle
6	chr19:44122600-44124600	Active TSS	Psoas Muscle	Psoas
7	chr19:44122600-44124600	Flanking Active TSS	HMEC	breast
8	chr19:44122600-44124800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:44122800-44124200	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr19:44122800-44124200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr19:44122800-44124200	Active TSS	Colonic Mucosa	Colon
12	chr19:44122800-44124400	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr19:44122800-44124400	Active TSS	Fetal Intestine Large	intestine
14	chr19:44122800-44124600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:44122800-44124600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:44122800-44124600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:44122800-44124800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:44123000-44124200	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr19:44123000-44124400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr19:44123000-44124400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:44123000-44124400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr19:44123000-44124400	Active TSS	Placenta Amnion	Placenta Amnion
23	chr19:44123000-44124600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr19:44123000-44124600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:44123000-44124600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:44123000-44124600	Active TSS	Aorta	Aorta
27	chr19:44123000-44124600	Active TSS	Ovary	ovary
28	chr19:44123000-44124800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr19:44123200-44124000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
30	chr19:44123200-44124000	Active TSS	Lung	lung
31	chr19:44123200-44124200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:44123200-44124200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:44123200-44124200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:44123200-44124200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:44123200-44124200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:44123200-44124200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr19:44123200-44124200	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr19:44123200-44124200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:44123200-44124200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:44123200-44124200	Active TSS	Esophagus	oesophagus
41	chr19:44123200-44124200	Active TSS	Fetal Brain Male	brain
42	chr19:44123200-44124200	Active TSS	Fetal Heart	heart
43	chr19:44123200-44124200	Active TSS	Fetal Intestine Small	intestine
44	chr19:44123200-44124200	Active TSS	Fetal Kidney	kidney
45	chr19:44123200-44124200	Active TSS	Fetal Lung	lung
46	chr19:44123200-44124200	Active TSS	Fetal Muscle Leg	muscle
47	chr19:44123200-44124200	Active TSS	Fetal Stomach	stomach
48	chr19:44123200-44124200	Active TSS	Left Ventricle	heart
49	chr19:44123200-44124200	Active TSS	Rectal Smooth Muscle	rectum
50	chr19:44123200-44124200	Active TSS	Small Intestine	intestine

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