Variant report

Variant	rs490498
Chromosome Location	chr1:155880952-155880953
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	POLR2A	chr1:155880916-155881319	Raji	blood:	n/a	n/a
2	MYBL2	chr1:155880904-155881594	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:155880500-155882029	Hela-S3	cervix:	n/a	n/a
4	YY1	chr1:155880909-155881417	SK-N-SH_RA	brain:	n/a	chr1:155881156-155881178 chr1:155880985-155880996 chr1:155881166-155881178
5	SIN3AK20	chr1:155880862-155881589	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr1:155880607-155881200	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:155880891-155881322	Gliobla	brain:	n/a	n/a
8	SMC3	chr1:155880464-155881484	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:155880908-155882410	HepG2	liver:	n/a	n/a
10	USF2	chr1:155880574-155881249	GM12878	blood:	n/a	chr1:155880988-155881004 chr1:155880788-155880799
11	POLR2A	chr1:155880856-155881395	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:155880873-155881561	HL-60	blood:	n/a	n/a
13	ZMIZ1	chr1:155880605-155881443	K562	blood:	n/a	n/a
14	REST	chr1:155880214-155881594	H1-neurons	neurons:	n/a	n/a
15	POLR2A	chr1:155880848-155881388	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:155880804-155882518	GM12892	blood:	n/a	n/a
17	ATF1	chr1:155880621-155881404	K562	blood:	n/a	n/a
18	YY1	chr1:155880803-155881443	HepG2	liver:	n/a	chr1:155881156-155881178 chr1:155880985-155880996 chr1:155881166-155881178
19	MAX	chr1:155880605-155881448	Hela-S3	cervix:	n/a	chr1:155881235-155881245 chr1:155880790-155880799
20	BCL3	chr1:155880462-155882083	A549	lung:	n/a	chr1:155881004-155881013
21	NFATC1	chr1:155880851-155882008	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:155880911-155881503	GM12892	blood:	n/a	n/a
23	USF1	chr1:155880490-155881213	SK-N-SH	brain:	n/a	chr1:155880988-155881004 chr1:155880788-155880799
24	POU2F2	chr1:155880951-155881452	GM12891	blood:	n/a	chr1:155880990-155881002 chr1:155880981-155880993
25	POLR2A	chr1:155880402-155882368	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr1:155880656-155882047	GM12878	blood:	n/a	n/a
27	CHD2	chr1:155880441-155881848	K562	blood:	n/a	n/a
28	PML	chr1:155880951-155881526	K562	blood:	n/a	n/a
29	CREB1	chr1:155880829-155881546	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:155880309-155882587	MCF-7	breast:	n/a	n/a
31	MAZ	chr1:155880469-155881463	Hela-S3	cervix:	n/a	chr1:155881235-155881245 chr1:155880790-155880799
32	POLR2A	chr1:155880948-155881535	Hela-S3	cervix:	n/a	n/a
33	SIN3A	chr1:155880420-155881455	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr1:155880882-155881550	A549	lung:	n/a	n/a
35	ELF1	chr1:155880915-155881510	K562	blood:	n/a	n/a
36	PBX3	chr1:155880837-155881411	A549	lung:	n/a	n/a
37	FOXM1	chr1:155880514-155881803	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:155880405-155882468	K562	blood:	n/a	n/a
39	CTCF	chr1:155880940-155881090	NHDF-neo	bronchial:	n/a	n/a
40	JUND	chr1:155880562-155881426	K562	blood:	n/a	n/a
41	POLR2A	chr1:155880601-155882023	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr1:155880950-155881465	NB4	blood:	n/a	n/a
43	YY1	chr1:155880895-155881474	SK-N-SH	brain:	n/a	chr1:155881156-155881178 chr1:155880985-155880996 chr1:155881166-155881178
44	POLR2A	chr1:155880679-155881895	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:155880872-155882448	GM12892	blood:	n/a	n/a
46	POLR2A	chr1:155880780-155882340	A549	lung:	n/a	n/a
47	ELF1	chr1:155880837-155881561	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:155880638-155882512	Hela-S3	cervix:	n/a	n/a
49	MAX	chr1:155880624-155881276	K562	blood:	n/a	chr1:155881235-155881245 chr1:155880790-155880799
50	HCFC1	chr1:155880163-155883715	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155825653..155829252-chr1:155877943..155882760,5	MCF-7	breast:
2	chr1:155879962..155882698-chr1:155885713..155888748,6	MCF-7	breast:
3	chr1:155879661..155882760-chr1:155946571..155949454,3	K562	blood:
4	chr1:155879409..155881796-chr1:155901375..155905401,4	MCF-7	breast:
5	chr1:155878384..155883302-chr1:155900472..155905868,7	K562	blood:
6	chr1:155880593..155881366-chr12:7053427..7053939,2	Hela-S3	cervix:
7	chr1:155825368..155829605-chr1:155879516..155883021,7	K562	blood:
8	chr1:155823442..155829143-chr1:155879989..155882670,6	MCF-7	breast:
9	chr1:155880615..155881579-chr7:21984391..21985346,2	Hela-S3	cervix:
10	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:
11	chr1:155879114..155881367-chr1:155902425..155905245,4	MCF-7	breast:

Variant related genes	Relation type
RIT1	TF binding region
ENSG00000132680	Chromatin interaction
ENSG00000116580	Chromatin interaction
ENSG00000132718	Chromatin interaction
ENSG00000164649	Chromatin interaction
ENSG00000116584	Chromatin interaction
ENSG00000273002	Chromatin interaction
ENSG00000272173	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10796955	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11264422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12024880	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12027412	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12563627	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1749405	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1889532	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2993207	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3856261	0.88[JPT][hapmap]
rs4661151	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4661175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4661218	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs488079	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs539602	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625658	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs639398	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs656247	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs656737	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs670523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729022	0.88[CEU][hapmap];0.83[MEX][hapmap]
rs7538214	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs821551	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap]
rs822478	1.00[ASW][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs822504	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs822505	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs822508	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[MEX][hapmap]
rs928596	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs490498	YY1AP1	cis	cerebellum	SCAN
rs490498	RIT1	cis	cerebellum	SCAN
rs490498	SPRR3	cis	parietal	SCAN
rs490498	RIT1	cis	Thyroid	GTEx
rs490498	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs490498	ROBLD3	cis	parietal	SCAN
rs490498	PRUNE	cis	cerebellum	SCAN
rs490498	UBQLN4	trans	parietal	SCAN
rs490498	FAM189B	cis	cerebellum	SCAN
rs490498	SLC39A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155879400-155881600	Active TSS	Rectal Smooth Muscle	rectum
2	chr1:155879600-155881400	Active TSS	Esophagus	oesophagus
3	chr1:155879800-155881400	Active TSS	Fetal Brain Male	brain
4	chr1:155879800-155881600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:155880000-155881200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:155880000-155881200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:155880000-155881400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:155880000-155881400	Active TSS	Brain Germinal Matrix	brain
9	chr1:155880000-155881400	Active TSS	Fetal Intestine Large	intestine
10	chr1:155880000-155881400	Active TSS	HSMMtube	muscle
11	chr1:155880000-155881600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:155880000-155881600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:155880000-155881600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr1:155880000-155881600	Active TSS	Aorta	Aorta
15	chr1:155880000-155881600	Active TSS	Right Atrium	heart
16	chr1:155880200-155881200	Active TSS	Muscle Satellite Cultured Cells	--
17	chr1:155880200-155881200	Active TSS	Lung	lung
18	chr1:155880200-155881200	Active TSS	HepG2	liver
19	chr1:155880200-155881200	Active TSS	NHLF	lung
20	chr1:155880200-155881400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr1:155880200-155881400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:155880200-155881400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr1:155880200-155881400	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:155880200-155881400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:155880200-155881400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:155880200-155881400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:155880200-155881400	Active TSS	Colonic Mucosa	Colon
28	chr1:155880200-155881400	Active TSS	Fetal Stomach	stomach
29	chr1:155880200-155881600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr1:155880200-155881600	Active TSS	Left Ventricle	heart
31	chr1:155880200-155881600	Active TSS	Ovary	ovary
32	chr1:155880200-155881600	Active TSS	Right Ventricle	heart
33	chr1:155880200-155881800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:155880400-155881200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:155880400-155881200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:155880400-155881200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:155880400-155881200	Active TSS	Gastric	stomach
38	chr1:155880400-155881200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:155880400-155881200	Active TSS	Small Intestine	intestine
40	chr1:155880400-155881200	Active TSS	Stomach Mucosa	stomach
41	chr1:155880400-155881200	Active TSS	A549	lung
42	chr1:155880400-155881400	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr1:155880400-155881400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:155880400-155881400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:155880400-155881400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:155880400-155881400	Active TSS	Brain Anterior Caudate	brain
47	chr1:155880400-155881400	Active TSS	Brain Hippocampus Middle	brain
48	chr1:155880400-155881400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:155880400-155881400	Active TSS	Fetal Kidney	kidney
50	chr1:155880400-155881400	Active TSS	NHDF-Ad	bronchial

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