Variant report

Variant	rs376890440
Chromosome Location	chr3:98250382-98250383
allele	C/T
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	MTA3	chr3:98249535-98254032	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:98248620-98252823	GM12892	blood:	n/a	n/a
3	STAT5A	chr3:98250364-98253431	GM12878	blood:	n/a	n/a
4	STAT3	chr3:98250158-98251060	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:98248655-98253486	GM15510	blood:	n/a	n/a
6	RCOR1	chr3:98250097-98251228	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:98249565-98253944	GM18951	blood:	n/a	n/a
8	POLR2A	chr3:98248658-98256543	GM18505	blood:	n/a	n/a
9	POU2F2	chr3:98250355-98252461	GM12878	blood:	n/a	chr3:98250619-98250629 chr3:98250616-98250630 chr3:98250619-98250629 chr3:98250618-98250628 chr3:98250618-98250630 chr3:98250612-98250634 chr3:98250617-98250630 chr3:98250620-98250627 chr3:98250616-98250631 chr3:98250619-98250628
10	CEBPB	chr3:98250202-98252695	GM12878	blood:	n/a	n/a
11	MXI1	chr3:98250141-98251489	GM12878	blood:	n/a	n/a
12	FOXM1	chr3:98250317-98251952	GM12878	blood:	n/a	n/a
13	NFIC	chr3:98250335-98251055	GM12878	blood:	n/a	chr3:98250610-98250638
14	EP300	chr3:98250381-98251108	GM12878	blood:	n/a	chr3:98250388-98250398 chr3:98250509-98250523
15	RUNX3	chr3:98250052-98252812	GM12878	blood:	n/a	chr3:98250633-98250642 chr3:98250633-98250642
16	MAZ	chr3:98249802-98252037	GM12878	blood:	n/a	n/a
17	IRF3	chr3:98250207-98250753	GM12878	blood:	n/a	chr3:98250513-98250522 chr3:98250514-98250524
18	POLR2A	chr3:98249459-98253009	GM12891	blood:	n/a	n/a
19	POLR2A	chr3:98248619-98253488	GM12892	blood:	n/a	n/a
20	RUNX3	chr3:98250085-98251091	GM12878	blood:	n/a	chr3:98250633-98250642 chr3:98250633-98250642
21	POLR2A	chr3:98248683-98253982	GM19099	blood:	n/a	n/a
22	FOXM1	chr3:98250006-98252764	GM12878	blood:	n/a	n/a
23	PML	chr3:98245909-98254043	GM12878	blood:	n/a	chr3:98253390-98253398
24	POLR2A	chr3:98248613-98253578	GM12892	blood:	n/a	n/a
25	POLR2A	chr3:98248690-98256144	GM19193	blood:	n/a	n/a
26	POLR2A	chr3:98248444-98256619	GM12878	blood:	n/a	n/a
27	NFATC1	chr3:98248840-98253424	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:98249471-98252678	GM12891	blood:	n/a	n/a
29	TBL1XR1	chr3:98250056-98252476	GM12878	blood:	n/a	n/a
30	ZNF384	chr3:98250269-98250964	GM12878	blood:	n/a	chr3:98250520-98250528
31	CREB1	chr3:98250264-98252480	GM12878	blood:	n/a	n/a
32	ATF2	chr3:98249967-98252577	GM12878	blood:	n/a	n/a
33	NFYB	chr3:98250305-98251033	GM12878	blood:	n/a	chr3:98250655-98250665
34	POLR2A	chr3:98248626-98253505	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:98248630-98254033	GM12878	blood:	n/a	n/a
36	NFATC1	chr3:98248493-98253590	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:98248622-98252794	GM12878	blood:	n/a	n/a
38	EBF1	chr3:98250304-98251523	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:98248610-98252751	GM12891	blood:	n/a	n/a
40	BHLHE40	chr3:98249324-98251183	GM12878	blood:	n/a	n/a
41	STAT5A	chr3:98250360-98253480	GM12878	blood:	n/a	n/a
42	BCLAF1	chr3:98250167-98253505	GM12878	blood:	n/a	chr3:98250514-98250523
43	TBP	chr3:98249482-98252493	GM12878	blood:	n/a	n/a
44	CUX1	chr3:98249608-98250960	GM12878	blood:	n/a	n/a
45	ATF2	chr3:98250379-98252988	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:98248703-98256575	GM12892	blood:	n/a	n/a
47	CHD1	chr3:98246186-98256496	GM12878	blood:	n/a	n/a
48	POLR2A	chr3:98248491-98253508	GM12892	blood:	n/a	n/a
49	POLR2A	chr3:98248676-98253986	GM12891	blood:	n/a	n/a
50	NFIC	chr3:98250026-98256659	GM12878	blood:	n/a	chr3:98252160-98252176 chr3:98250228-98250256 chr3:98250610-98250638 chr3:98252159-98252176

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:98250382-98250432	AG04450	lung:	fetal
2	chr3:98250382-98250432	HIPEpiC	eye:	n/a
3	chr3:98250382-98250432	RPTEC	kidney:	n/a
4	chr3:98250382-98250432	MCF10A-Er-Src	breast:	n/a
5	chr3:98250382-98250432	HNPCEpiC	eye:	n/a
6	chr3:98250382-98250432	Jurkat	blood:	n/a
7	chr3:98250382-98250432	HRCEpiC	kidney:	n/a
8	chr3:98250382-98250432	GM06990	blood:	n/a
9	chr3:98250382-98250432	ProgFib	skin:	n/a
10	chr3:98250382-98250432	NB4	blood:	n/a
11	chr3:98250382-98250432	T-47D	breast:	n/a
12	chr3:98250382-98250432	ECC-1	luminal epithelium:	n/a
13	chr3:98250382-98250432	LNCaP	prostate:	n/a
14	chr3:98250382-98250432	PANC-1	pancreas:	n/a
15	chr3:98250382-98250432	CMK	blood:	n/a
16	chr3:98250382-98250432	SK-N-SH	brain:	n/a
17	chr3:98250382-98250432	ovcar-3	ovarian:	n/a
18	chr3:98250382-98250432	HCPEpiC	choroid plexus:	n/a
19	chr3:98250382-98250432	NH-A	brain:	n/a
20	chr3:98250382-98250432	BE2_C	brain:	n/a
21	chr3:98250382-98250432	GM12878	blood:	n/a
22	chr3:98250382-98250432	MCF-7	breast:	n/a
23	chr3:98250382-98250432	BJ	skin:	n/a
24	chr3:98250382-98250432	Hepatocyte	liver:	n/a
25	chr3:98250382-98250432	SK-N-MC	brain:	n/a
26	chr3:98250382-98250432	PrEC	prostate:	n/a
27	chr3:98250382-98250432	SKMC	muscle:	n/a
28	chr3:98250382-98250432	GM12892	blood:	n/a
29	chr3:98250382-98250432	HAEpiC	amniotic membrane:	n/a
30	chr3:98250382-98250432	U87	brain:	n/a
31	chr3:98250382-98250432	AoSMC	blood vessel:	n/a
32	chr3:98250382-98250432	H1-hESC	embryonic stem cell:	embryo
33	chr3:98250382-98250432	HRPEpiC	eye:	n/a
34	chr3:98250382-98250432	HUVEC	blood vessel:	n/a
35	chr3:98250382-98250432	SK-N-SH_RA	brain:	n/a
36	chr3:98250382-98250432	Hela-S3	cervix:	n/a
37	chr3:98250382-98250432	HCM	heart:	n/a
38	chr3:98250382-98250432	HL-60	blood:	n/a
39	chr3:98250382-98250432	AG09319	gingival:	n/a
40	chr3:98250382-98250432	HEEpiC	esophagus:	n/a
41	chr3:98250382-98250432	GM12891	blood:	n/a
42	chr3:98250382-98250432	K562	blood:	n/a
43	chr3:98250382-98250432	AG09309	skin:	n/a
44	chr3:98250382-98250432	HMEC	breast:	n/a
45	chr3:98250382-98250432	NHBE	bronchial:	n/a
46	chr3:98250382-98250432	AG10803	skin:	n/a
47	chr3:98250382-98250432	HEK293	kidney:	embryo
48	chr3:98250382-98250432	AG04449	skin:	fetal
49	chr3:98250382-98250432	A549	lung:	n/a
50	chr3:98250382-98250432	IMR90	lung:	fetal

Variant related genes	Relation type
GPR15	TF binding region
GPR15	CpG island

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528056	chr3:98101101-98317836	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv520503	chr3:98102801-98317836	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv834774	chr3:98108423-98274064	Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv834775	chr3:98170059-98367552	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv236502	chr3:98250046-98254624	Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98242200-98250800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr3:98249200-98250800	Active TSS	GM12878-XiMat	blood
3	chr3:98249200-98250800	Weak transcription	K562	blood
4	chr3:98249200-98251200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:98249800-98250400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:98250200-98250600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:98250200-98256200	Active TSS	Rectal Mucosa Donor 29	rectum

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