Variant report

Variant	rs3744992
Chromosome Location	chr18:43684657-43684658
allele	A/C
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	POLR2A	chr18:43684047-43685014	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr18:43684056-43684902	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr18:43684000-43684921	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr18:43684480-43684857	HepG2	liver:	n/a	n/a
5	CHD2	chr18:43684102-43684712	Hela-S3	cervix:	n/a	chr18:43684362-43684372
6	SIN3AK20	chr18:43684056-43684949	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr18:43684104-43684714	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr18:43684004-43684903	NB4	blood:	n/a	chr18:43684303-43684313
9	MAX	chr18:43683884-43684740	A549	lung:	n/a	chr18:43684303-43684313
10	POLR2A	chr18:43684007-43684960	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr18:43683868-43684689	U87	brain:	n/a	n/a
12	HCFC1	chr18:43684013-43685024	K562	blood:	n/a	n/a
13	RELA	chr18:43684088-43684892	GM15510	blood:	n/a	n/a
14	TAF1	chr18:43684070-43684799	SK-N-SH	brain:	n/a	n/a
15	TBP	chr18:43684056-43684978	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr18:43683911-43684903	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr18:43683912-43685025	PBDE	blood:	n/a	n/a
18	TBP	chr18:43684031-43684956	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr18:43684096-43684793	GM12891	blood:	n/a	n/a
20	POLR2A	chr18:43684130-43684773	HepG2	liver:	n/a	n/a
21	YY1	chr18:43684065-43684673	GM12878	blood:	n/a	n/a
22	POLR2A	chr18:43684084-43684824	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr18:43684066-43684991	H1-neurons	neurons:	n/a	n/a
24	MYC	chr18:43684629-43684694	MCF-7	breast:	n/a	n/a
25	POLR2A	chr18:43684154-43684920	ECC-1	luminal epithelium:	n/a	n/a
26	GABPA	chr18:43684069-43684942	MCF-7	breast:	n/a	chr18:43684303-43684312
27	E2F6	chr18:43683841-43684770	H1-hESC	embryonic stem cell:	n/a	chr18:43684412-43684424 chr18:43684149-43684160
28	ZNF263	chr18:43684327-43685160	HEK293-T-REx	kidney:	n/a	chr18:43684502-43684523
29	POLR2A	chr18:43684100-43684954	PANC-1	pancreas:	n/a	n/a
30	HCFC1	chr18:43683835-43685318	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr18:43683997-43684767	HepG2	liver:	n/a	n/a
32	POLR2A	chr18:43684041-43684847	GM15510	blood:	n/a	n/a
33	POLR2A	chr18:43683998-43684931	SK-N-SH	brain:	n/a	n/a
34	GABPA	chr18:43684584-43684793	Hela-S3	cervix:	n/a	n/a
35	UBTF	chr18:43684067-43684951	K562	blood:	n/a	n/a
36	ELK4	chr18:43684180-43684751	Hela-S3	cervix:	n/a	n/a
37	REST	chr18:43684443-43684837	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr18:43684043-43684758	GM12878	blood:	n/a	n/a
39	POLR2A	chr18:43684066-43684883	GM18526	blood:	n/a	n/a
40	POLR2A	chr18:43683997-43684886	Raji	blood:	n/a	n/a
41	MYC	chr18:43684053-43684752	NB4	blood:	n/a	chr18:43684303-43684313
42	POLR2A	chr18:43684092-43684906	GM18951	blood:	n/a	n/a
43	ZNF143	chr18:43684004-43684971	GM12878	blood:	n/a	chr18:43684738-43684756
44	CTCF	chr18:43684620-43684770	HCPEpiC	choroid plexus:	n/a	n/a
45	HA-E2F1	chr18:43684144-43684854	Hela-S3	cervix:	n/a	chr18:43684359-43684370 chr18:43684334-43684345 chr18:43684412-43684424
46	SIN3AK20	chr18:43684177-43684774	PANC-1	pancreas:	n/a	n/a
47	ELF1	chr18:43684562-43684823	K562	blood:	n/a	chr18:43684770-43684782
48	YY1	chr18:43684103-43684782	K562	blood:	n/a	n/a
49	E2F1	chr18:43684148-43684837	Hela-S3	cervix:	n/a	chr18:43684359-43684370 chr18:43684334-43684345 chr18:43684412-43684424
50	MAX	chr18:43683929-43684915	HepG2	liver:	n/a	chr18:43684303-43684313

No.	Distal block	Cell Line	Cell type
1	chr18:43677240..43681670-chr18:43684014..43685946,4	K562	blood:
2	chr18:43676160..43680812-chr18:43682051..43685941,8	K562	blood:
3	chr18:43676858..43680433-chr18:43682158..43685518,5	MCF-7	breast:

Variant related genes	Relation type
ATP5A1	TF binding region
ENSG00000152234	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11876373	0.84[ASN][1000 genomes]
rs12606184	0.86[ASN][1000 genomes]
rs12607480	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12709735	0.83[ASN][1000 genomes]
rs12954742	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs12959543	0.86[ASN][1000 genomes]
rs12963169	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs1658908	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1791407	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs1791413	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs1791414	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs1866321	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1866322	0.91[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1964984	0.80[ASN][1000 genomes]
rs2467669	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515639	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578184	0.93[ASN][1000 genomes]
rs2578187	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.93[ASN][1000 genomes]
rs2578188	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2578189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2578190	0.96[ASN][1000 genomes]
rs2578192	0.84[ASN][1000 genomes]
rs2578193	0.96[ASN][1000 genomes]
rs28497462	0.88[ASN][1000 genomes]
rs2850644	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2850646	0.84[ASN][1000 genomes]
rs2852362	0.94[ASN][1000 genomes]
rs2852363	0.95[ASN][1000 genomes]
rs28524126	0.84[ASN][1000 genomes]
rs2853801	0.96[ASN][1000 genomes]
rs2853802	0.96[ASN][1000 genomes]
rs28715068	0.91[ASN][1000 genomes]
rs28768435	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28805990	0.96[ASN][1000 genomes]
rs28809822	0.90[ASN][1000 genomes]
rs35122885	0.97[ASN][1000 genomes]
rs35338711	0.88[ASN][1000 genomes]
rs35360831	0.92[ASN][1000 genomes]
rs35657986	0.84[ASN][1000 genomes]
rs3753069	0.85[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4243278	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4260155	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4274509	0.87[CHB][hapmap]
rs474878	0.96[ASN][1000 genomes]
rs4890313	0.86[CHB][hapmap]
rs4890617	0.82[CHB][hapmap];0.80[MEX][hapmap]
rs4890618	0.82[CHB][hapmap]
rs4890619	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs4890620	0.91[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap]
rs4890624	0.96[ASN][1000 genomes]
rs4890625	0.85[ASN][1000 genomes]
rs59082804	0.94[ASN][1000 genomes]
rs60986007	0.84[ASN][1000 genomes]
rs71364518	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7226736	0.88[ASN][1000 genomes]
rs7226742	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7229971	0.83[ASN][1000 genomes]
rs7230180	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7233665	0.90[ASN][1000 genomes]
rs8083916	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8085233	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs8085773	0.96[ASN][1000 genomes]
rs8088422	0.83[ASN][1000 genomes]
rs8096256	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs8096643	0.86[ASN][1000 genomes]
rs9946831	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9950234	0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs9950343	0.86[CHB][hapmap]
rs9952157	0.81[ASN][1000 genomes]
rs9954133	0.88[ASN][1000 genomes]
rs9954534	0.84[ASN][1000 genomes]
rs9955008	0.87[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs9956803	0.86[CHB][hapmap]
rs9958257	0.83[ASN][1000 genomes]
rs9965365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9965812	0.87[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs9966603	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv962965	chr18:43678008-43706302	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3744992	IER3IP1	cis	cerebellum	SCAN
rs3744992	HAUS1	cis	parietal	SCAN
rs3744992	HAUS1	cis	cerebellum	SCAN
rs3744992	HAUS1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43683800-43684800	Active TSS	Brain Angular Gyrus	brain
2	chr18:43683800-43685000	Active TSS	Brain Substantia Nigra	brain
3	chr18:43683800-43685200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr18:43683800-43685400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr18:43683800-43685400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr18:43683800-43685400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr18:43683800-43685400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr18:43683800-43685400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr18:43683800-43685400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr18:43683800-43685400	Active TSS	NHDF-Ad	bronchial
11	chr18:43683800-43685600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:43683800-43685600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr18:43683800-43685600	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr18:43683800-43685800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr18:43683800-43685800	Active TSS	Brain Germinal Matrix	brain
16	chr18:43684000-43684800	Active TSS	Primary T cells from cord blood	blood
17	chr18:43684000-43684800	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr18:43684000-43684800	Active TSS	Rectal Smooth Muscle	rectum
19	chr18:43684000-43685000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr18:43684000-43685000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr18:43684000-43685000	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr18:43684000-43685000	Active TSS	Brain Anterior Caudate	brain
23	chr18:43684000-43685000	Active TSS	Duodenum Mucosa	Duodenum
24	chr18:43684000-43685000	ZNF genes & repeats	Fetal Brain Male	brain
25	chr18:43684000-43685000	Active TSS	Left Ventricle	heart
26	chr18:43684000-43685000	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr18:43684000-43685000	Active TSS	HSMMtube	muscle
28	chr18:43684000-43685200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr18:43684000-43685200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr18:43684000-43685200	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr18:43684000-43685200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr18:43684000-43685200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr18:43684000-43685200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr18:43684000-43685200	Active TSS	Aorta	Aorta
35	chr18:43684000-43685200	Active TSS	Brain Cingulate Gyrus	brain
36	chr18:43684000-43685200	Active TSS	Brain Hippocampus Middle	brain
37	chr18:43684000-43685200	Active TSS	Colonic Mucosa	Colon
38	chr18:43684000-43685200	Active TSS	Fetal Intestine Large	intestine
39	chr18:43684000-43685200	Active TSS	Fetal Intestine Small	intestine
40	chr18:43684000-43685200	Active TSS	Psoas Muscle	Psoas
41	chr18:43684000-43685200	Active TSS	Right Atrium	heart
42	chr18:43684000-43685200	Active TSS	Right Ventricle	heart
43	chr18:43684000-43685200	Active TSS	HSMM	muscle
44	chr18:43684000-43685400	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr18:43684000-43685400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr18:43684000-43685400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr18:43684000-43685400	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr18:43684000-43685400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr18:43684000-43685400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr18:43684000-43685400	Active TSS	Pancreatic Islets	Pancreatic Islet

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