Variant report

Variant	rs2298735
Chromosome Location	chr4:100815617-100815618
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:364)
CpG islands
(count:122)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:364 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:100815176-100816143	HUVEC	blood vessel:	n/a	n/a
2	ZKSCAN1	chr4:100815509-100815632	Hela-S3	cervix:	n/a	n/a
3	MAX	chr4:100815356-100815844	H1-hESC	embryonic stem cell:	n/a	n/a
4	ATF2	chr4:100815272-100816060	GM12878	blood:	n/a	n/a
5	MXI1	chr4:100815209-100816049	HepG2	liver:	n/a	n/a
6	YY1	chr4:100814966-100815784	GM12892	blood:	n/a	n/a
7	ARID3A	chr4:100815505-100815618	HepG2	liver:	n/a	n/a
8	YY1	chr4:100815397-100815690	GM12878	blood:	n/a	n/a
9	SP1	chr4:100815376-100815944	GM12878	blood:	n/a	n/a
10	ZBTB7A	chr4:100815520-100815763	K562	blood:	n/a	n/a
11	POLR2A	chr4:100815237-100816180	PFSK-1	brain:	n/a	n/a
12	USF1	chr4:100815270-100815910	SK-N-SH_RA	brain:	n/a	n/a
13	JUND	chr4:100815430-100815905	A549	lung:	n/a	n/a
14	IRF1	chr4:100815374-100815978	K562	blood:	n/a	n/a
15	POLR2A	chr4:100815326-100816196	HL-60	blood:	n/a	n/a
16	TCF12	chr4:100815331-100816064	ECC-1	luminal epithelium:	n/a	chr4:100815331-100815338
17	MYC	chr4:100815380-100815696	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT1	chr4:100815376-100816049	GM12878	blood:	n/a	chr4:100815784-100815791
19	POLR2A	chr4:100815015-100816148	GM12878	blood:	n/a	n/a
20	CREB1	chr4:100815405-100815785	A549	lung:	n/a	n/a
21	MAZ	chr4:100815270-100815921	HepG2	liver:	n/a	n/a
22	POU2F2	chr4:100815046-100815693	GM12891	blood:	n/a	chr4:100815439-100815451
23	USF1	chr4:100815193-100815988	ECC-1	luminal epithelium:	n/a	n/a
24	CREB1	chr4:100815313-100815935	K562	blood:	n/a	n/a
25	USF1	chr4:100815211-100815830	K562	blood:	n/a	n/a
26	ETS1	chr4:100815227-100815717	K562	blood:	n/a	chr4:100815640-100815653 chr4:100815599-100815612 chr4:100815601-100815612 chr4:100815296-100815309
27	ELK1	chr4:100815470-100815673	K562	blood:	n/a	n/a
28	TBP	chr4:100815413-100815656	Hela-S3	cervix:	n/a	n/a
29	BCL3	chr4:100815341-100816020	GM12878	blood:	n/a	n/a
30	ELF1	chr4:100815484-100815852	K562	blood:	n/a	n/a
31	GABPA	chr4:100815331-100815878	HL-60	blood:	n/a	chr4:100815756-100815767 chr4:100815753-100815767
32	POLR2A	chr4:100815269-100815679	U87	brain:	n/a	n/a
33	GABPA	chr4:100815222-100815802	A549	lung:	n/a	chr4:100815756-100815767 chr4:100815753-100815767
34	NR2C2	chr4:100815209-100815793	HepG2	liver:	n/a	n/a
35	MAX	chr4:100815222-100815850	ECC-1	luminal epithelium:	n/a	n/a
36	MYC	chr4:100815380-100815933	NB4	blood:	n/a	n/a
37	NFIC	chr4:100815239-100816066	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr4:100815279-100815914	K562	blood:	n/a	n/a
39	POLR2A	chr4:100815204-100816092	H1-hESC	embryonic stem cell:	n/a	n/a
40	NFIC	chr4:100815224-100815690	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:100815314-100816004	HepG2	liver:	n/a	n/a
42	YY1	chr4:100814985-100815683	GM12878	blood:	n/a	n/a
43	TAF1	chr4:100815369-100815674	PFSK-1	brain:	n/a	n/a
44	CHD2	chr4:100815321-100815937	Hela-S3	cervix:	n/a	n/a
45	TAF1	chr4:100815367-100815675	H1-hESC	embryonic stem cell:	n/a	n/a
46	FOSL2	chr4:100815374-100816064	HepG2	liver:	n/a	n/a
47	HMGN3	chr4:100815503-100816149	K562	blood:	n/a	n/a
48	USF1	chr4:100815160-100816063	HCT-116	colon:	n/a	n/a
49	USF2	chr4:100815161-100815944	GM12878	blood:	n/a	chr4:100815569-100815580
50	BCL3	chr4:100815216-100815755	A549	lung:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:100815590-100815640	NHBE	bronchial:	n/a
2	chr4:100815590-100815640	NHDF-neo	bronchial:	n/a
3	chr4:100815590-100815640	HCPEpiC	choroid plexus:	n/a
4	chr4:100815590-100815640	AG04449	skin:	fetal
5	chr4:100815570-100815620	AG09319	gingival:	n/a
6	chr4:100815590-100815640	NH-A	brain:	n/a
7	chr4:100815590-100815640	HNPCEpiC	eye:	n/a
8	chr4:100815590-100815640	T-47D	breast:	n/a
9	chr4:100815590-100815640	A549	lung:	n/a
10	chr4:100815590-100815640	HL-60	blood:	n/a
11	chr4:100815590-100815640	BE2_C	brain:	n/a
12	chr4:100815590-100815640	GM12891	blood:	n/a
13	chr4:100815570-100815620	AG04449	skin:	fetal
14	chr4:100815590-100815640	NT2-D1	testis:	n/a
15	chr4:100815570-100815620	PrEC	prostate:	n/a
16	chr4:100815570-100815620	HL-60	blood:	n/a
17	chr4:100815570-100815620	GM19239	blood:	n/a
18	chr4:100815570-100815620	IMR90	lung:	fetal
19	chr4:100815570-100815620	SK-N-SH	brain:	n/a
20	chr4:100815590-100815640	H1-hESC	embryonic stem cell:	embryo
21	chr4:100815590-100815640	HAEpiC	amniotic membrane:	n/a
22	chr4:100815570-100815620	RPTEC	kidney:	n/a
23	chr4:100815570-100815620	T-47D	breast:	n/a
24	chr4:100815590-100815640	Hepatocyte	liver:	n/a
25	chr4:100815570-100815620	ovcar-3	ovarian:	n/a
26	chr4:100815590-100815640	HRPEpiC	eye:	n/a
27	chr4:100815590-100815640	K562	blood:	n/a
28	chr4:100815590-100815640	RPTEC	kidney:	n/a
29	chr4:100815570-100815620	GM12891	blood:	n/a
30	chr4:100815570-100815620	U87	brain:	n/a
31	chr4:100815590-100815640	HCT-116	colon:	n/a
32	chr4:100815570-100815620	HNPCEpiC	eye:	n/a
33	chr4:100815590-100815640	U87	brain:	n/a
34	chr4:100815570-100815620	MCF10A-Er-Src	breast:	n/a
35	chr4:100815570-100815620	HMEC	breast:	n/a
36	chr4:100815590-100815640	HepG2	liver:	n/a
37	chr4:100815590-100815640	GM12878	blood:	n/a
38	chr4:100815570-100815620	BE2_C	brain:	n/a
39	chr4:100815590-100815640	CMK	blood:	n/a
40	chr4:100815590-100815640	GM06990	blood:	n/a
41	chr4:100815590-100815640	PANC-1	pancreas:	n/a
42	chr4:100815570-100815620	HEK293	kidney:	embryo
43	chr4:100815570-100815620	HepG2	liver:	n/a
44	chr4:100815570-100815620	AG10803	skin:	n/a
45	chr4:100815570-100815620	HIPEpiC	eye:	n/a
46	chr4:100815590-100815640	PrEC	prostate:	n/a
47	chr4:100815570-100815620	PANC-1	pancreas:	n/a
48	chr4:100815590-100815640	HUVEC	blood vessel:	n/a
49	chr4:100815590-100815640	LNCaP	prostate:	n/a
50	chr4:100815590-100815640	SAEC	small airway:	n/a

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:100813266..100817175-chr4:100865527..100871657,11	MCF-7	breast:
2	chr4:100814600..100817376-chr4:100869817..100872742,4	MCF-7	breast:
3	chr17:57970213..57970964-chr4:100815105..100815985,2	MCF-7	breast:
4	chr4:100815570..100818331-chr4:100848090..100849658,2	K562	blood:
5	chr4:100814213..100816552-chr4:100866797..100868818,3	MCF-7	breast:
6	chr4:100737221..100739559-chr4:100813734..100816080,3	MCF-7	breast:
7	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
8	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:
9	chr4:100482462..100485382-chr4:100814090..100816679,3	MCF-7	breast:

No data

Variant related genes	Relation type
LAMTOR3	TF binding region
LAMTOR3	CpG island
ENSG00000164032	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000164031	Chromatin interaction
ENSG00000138823	Chromatin interaction
ENSG00000145331	Chromatin interaction
ENSG00000070190	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000108443	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10026048	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097676	0.95[JPT][hapmap]
rs11097677	0.95[JPT][hapmap]
rs11732776	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935024	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11935399	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11939538	0.87[LWK][hapmap]
rs1365491	0.95[JPT][hapmap]
rs1365492	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.95[ASN][1000 genomes]
rs1365495	0.91[JPT][hapmap]
rs17029563	0.95[JPT][hapmap]
rs17029583	0.82[ASN][1000 genomes]
rs17029662	0.86[LWK][hapmap]
rs1863608	0.90[JPT][hapmap]
rs1896166	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961323	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1972698	0.95[JPT][hapmap]
rs2070738	0.85[CEU][hapmap]
rs2098937	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2114442	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2282588	0.91[JPT][hapmap]
rs28404345	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2866180	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28706589	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756087	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3775499	0.95[JPT][hapmap]
rs3775500	0.95[JPT][hapmap]
rs3775501	0.95[JPT][hapmap]
rs3775511	0.94[ASN][1000 genomes]
rs4699764	0.86[JPT][hapmap]
rs4699765	0.90[JPT][hapmap]
rs60978748	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532833	0.95[JPT][hapmap]
rs6532835	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6532836	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811559	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6814895	0.95[JPT][hapmap]
rs6848337	0.88[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6849599	0.87[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.94[MKK][hapmap];0.82[ASN][1000 genomes]
rs6854536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs715239	0.91[JPT][hapmap]
rs7675947	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7676564	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7684872	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7686428	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7689566	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7692416	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919132	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.92[ASN][1000 genomes]
rs919133	0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.92[ASN][1000 genomes]
rs9307242	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2298735	DAPP1	Cis_1M	lymphoblastoid	RTeQTL
rs2298735	NFKB1	cis	cerebellum	SCAN
rs2298735	DNAJB14	cis	parietal	SCAN
rs2298735	MAPKSP1	cis	parietal	SCAN
rs2298735	MAPKSP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100813200-100816600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:100814000-100816200	Active TSS	HSMM	muscle
3	chr4:100814200-100816000	Active TSS	HSMMtube	muscle
4	chr4:100814200-100816200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:100814200-100816200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:100814200-100816200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:100814200-100816200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:100814200-100816200	Active TSS	A549	lung
9	chr4:100814400-100816000	Active TSS	Pancreas	Pancrea
10	chr4:100814400-100816000	Active TSS	NHLF	lung
11	chr4:100814400-100816200	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr4:100814400-100816400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr4:100814400-100816400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr4:100814400-100816400	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr4:100814400-100816600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr4:100814600-100815800	Active TSS	HMEC	breast
17	chr4:100814600-100816000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:100814600-100816000	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr4:100814600-100816000	Active TSS	Fetal Intestine Large	intestine
20	chr4:100814600-100816000	Active TSS	NHDF-Ad	bronchial
21	chr4:100814600-100816200	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr4:100814600-100816200	Active TSS	Muscle Satellite Cultured Cells	--
23	chr4:100814600-100816200	Active TSS	Aorta	Aorta
24	chr4:100814600-100816200	Active TSS	Fetal Muscle Trunk	muscle
25	chr4:100814600-100816200	Active TSS	Ovary	ovary
26	chr4:100814600-100816200	Active TSS	Right Atrium	heart
27	chr4:100814600-100816400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr4:100814600-100816400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr4:100814600-100816400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:100814600-100816400	Active TSS	Psoas Muscle	Psoas
31	chr4:100814800-100815800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:100814800-100815800	Active TSS	K562	blood
33	chr4:100814800-100815800	Active TSS	NH-A	brain
34	chr4:100814800-100815800	Active TSS	NHEK	skin
35	chr4:100814800-100816000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:100814800-100816000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:100814800-100816000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:100814800-100816000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:100814800-100816000	Active TSS	Esophagus	oesophagus
40	chr4:100814800-100816000	Active TSS	Gastric	stomach
41	chr4:100814800-100816000	Active TSS	Lung	lung
42	chr4:100814800-100816000	Active TSS	Hela-S3	cervix
43	chr4:100814800-100816200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:100814800-100816200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr4:100814800-100816200	Active TSS	Colon Smooth Muscle	Colon
46	chr4:100814800-100816200	Active TSS	Fetal Kidney	kidney
47	chr4:100814800-100816200	Active TSS	Left Ventricle	heart
48	chr4:100814800-100816200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr4:100814800-100816200	Active TSS	Right Ventricle	heart
50	chr4:100814800-100816200	Active TSS	Stomach Mucosa	stomach

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