Variant report

Variant	rs73406084
Chromosome Location	chr7:97880763-97880764
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	CREB1	chr7:97880623-97882132	HepG2	liver:	n/a	n/a
2	MAX	chr7:97880734-97882118	MCF-7	breast:	n/a	n/a
3	NR2F2	chr7:97880704-97882234	MCF-7	breast:	n/a	n/a
4	RUNX3	chr7:97880467-97880832	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:97880225-97881989	GM18951	blood:	n/a	n/a
6	SP1	chr7:97880607-97882192	HCT-116	colon:	n/a	chr7:97881308-97881322 chr7:97881304-97881318 chr7:97881548-97881569
7	POLR2A	chr7:97880703-97882004	Raji	blood:	n/a	n/a
8	SIN3A	chr7:97880210-97882216	H1-hESC	embryonic stem cell:	n/a	chr7:97880924-97880935
9	CHD2	chr7:97880725-97881964	GM12878	blood:	n/a	n/a
10	MAX	chr7:97880650-97882021	ECC-1	luminal epithelium:	n/a	n/a
11	HCFC1	chr7:97880731-97882103	Hela-S3	cervix:	n/a	n/a
12	SIN3AK20	chr7:97880543-97882202	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr7:97880699-97882049	MCF-7	breast:	n/a	n/a
14	SIN3A	chr7:97880699-97881895	GM12878	blood:	n/a	chr7:97880924-97880935
15	MAX	chr7:97880641-97882183	MCF-7	breast:	n/a	n/a
16	TCF12	chr7:97880675-97882061	ECC-1	luminal epithelium:	n/a	chr7:97881275-97881282
17	EGR1	chr7:97880635-97882080	HCT-116	colon:	n/a	chr7:97881259-97881268 chr7:97881653-97881662 chr7:97881647-97881660 chr7:97881256-97881269
18	NFIC	chr7:97880550-97881881	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr7:97880628-97880912	GM12878	blood:	n/a	n/a
20	MAX	chr7:97880670-97882117	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr7:97880131-97882153	GM12878	blood:	n/a	n/a
22	ZEB1	chr7:97880704-97881985	GM12878	blood:	n/a	chr7:97881911-97881922 chr7:97881430-97881443
23	ZNF143	chr7:97880712-97881690	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr7:97880009-97880896	GM12892	blood:	n/a	n/a
25	PML	chr7:97880256-97880867	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:97880155-97882023	GM19193	blood:	n/a	n/a
27	ZBTB7A	chr7:97880592-97881599	ECC-1	luminal epithelium:	n/a	n/a
28	ZEB1	chr7:97880499-97882280	HepG2	liver:	n/a	chr7:97881911-97881922 chr7:97881430-97881443
29	FOXA1	chr7:97880648-97880870	T-47D	breast:	n/a	n/a
30	MAZ	chr7:97880167-97881961	GM12878	blood:	n/a	n/a
31	POLR2A	chr7:97880087-97882070	GM18505	blood:	n/a	n/a
32	POLR2A	chr7:97880052-97882017	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr7:97880104-97881979	GM12892	blood:	n/a	n/a
34	POLR2A	chr7:97880139-97881937	GM19099	blood:	n/a	n/a
35	TCF12	chr7:97880552-97881970	ECC-1	luminal epithelium:	n/a	chr7:97881275-97881282
36	POLR2A	chr7:97880123-97882176	HepG2	liver:	n/a	n/a
37	POLR2A	chr7:97879994-97882127	GM12891	blood:	n/a	n/a
38	SP1	chr7:97880509-97882159	HCT-116	colon:	n/a	chr7:97881308-97881322 chr7:97881304-97881318 chr7:97881548-97881569
39	NFIC	chr7:97880670-97881970	ECC-1	luminal epithelium:	n/a	n/a
40	MXI1	chr7:97880742-97882199	H1-hESC	embryonic stem cell:	n/a	n/a
41	MTA3	chr7:97880541-97881924	GM12878	blood:	n/a	n/a
42	ELF1	chr7:97880706-97882045	GM12878	blood:	n/a	chr7:97881653-97881664 chr7:97881533-97881542 chr7:97881653-97881664 chr7:97881652-97881665 chr7:97881654-97881663
43	EP300	chr7:97880634-97881980	ECC-1	luminal epithelium:	n/a	chr7:97881399-97881415 chr7:97880928-97880944 chr7:97881654-97881661

No.	Distal block	Cell Line	Cell type
1	chr7:97880638..97884180-chr7:98029742..98031678,3	MCF-7	breast:
2	chr7:97880609..97882891-chr7:97909884..97913133,3	MCF-7	breast:
3	chr7:97847018..97848537-chr7:97878984..97881844,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BAIAP2L1.1-1	chr7:97880226-97880860	NONHSAT122185
2	lnc-BAIAP2L1.1-1	chr7:97880731-97880860	NONHSAT122183

Variant related genes	Relation type
BRI3	TF binding region
ENSG00000205356	Chromatin interaction
ENSG00000006453	Chromatin interaction
ENSG00000164713	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10280984	1.00[AMR][1000 genomes]
rs12704968	1.00[AMR][1000 genomes]
rs1464739	1.00[AMR][1000 genomes]
rs1880303	1.00[AMR][1000 genomes]
rs1983439	1.00[AMR][1000 genomes]
rs2088171	1.00[AMR][1000 genomes]
rs2172885	1.00[AMR][1000 genomes]
rs4509254	1.00[AMR][1000 genomes]
rs4727387	1.00[AMR][1000 genomes]
rs4729411	1.00[AMR][1000 genomes]
rs4729433	1.00[AMR][1000 genomes]
rs6465652	1.00[AMR][1000 genomes]
rs6465656	1.00[AMR][1000 genomes]
rs6465659	1.00[AMR][1000 genomes]
rs6943900	1.00[AMR][1000 genomes]
rs6943971	1.00[AMR][1000 genomes]
rs6945999	1.00[AMR][1000 genomes]
rs6956383	1.00[AMR][1000 genomes]
rs6970100	1.00[AMR][1000 genomes]
rs6971967	1.00[AMR][1000 genomes]
rs6975661	1.00[AMR][1000 genomes]
rs7788829	1.00[AMR][1000 genomes]
rs7800032	1.00[AMR][1000 genomes]
rs7804326	1.00[AMR][1000 genomes]
rs7805804	1.00[AMR][1000 genomes]
rs903593	1.00[AMR][1000 genomes]
rs982466	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS 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	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv1800947	chr7:97857675-97889672	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97874000-97880800	Weak transcription	Ovary	ovary
2	chr7:97874200-97881000	Weak transcription	Aorta	Aorta
3	chr7:97877200-97880800	Enhancers	Spleen	Spleen
4	chr7:97877800-97880800	Weak transcription	Lung	lung
5	chr7:97879200-97881000	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr7:97879400-97880800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr7:97879400-97881200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr7:97879800-97881000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr7:97879800-97881000	Flanking Active TSS	Dnd41	blood
10	chr7:97879800-97881200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr7:97879800-97881200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr7:97879800-97881200	Flanking Active TSS	GM12878-XiMat	blood
13	chr7:97880000-97880800	Enhancers	Fetal Heart	heart
14	chr7:97880000-97880800	Flanking Active TSS	HepG2	liver
15	chr7:97880000-97881000	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr7:97880000-97881200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr7:97880000-97881200	Flanking Active TSS	Fetal Thymus	thymus
18	chr7:97880000-97881200	Flanking Active TSS	HUVEC	blood vessel
19	chr7:97880000-97881400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr7:97880000-97882800	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr7:97880200-97880800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:97880200-97880800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr7:97880200-97880800	Flanking Active TSS	Fetal Intestine Small	intestine
24	chr7:97880200-97880800	Active TSS	Gastric	stomach
25	chr7:97880200-97881000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:97880200-97881000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:97880200-97881000	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr7:97880200-97881000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr7:97880200-97881000	Flanking Active TSS	Fetal Brain Female	brain
30	chr7:97880200-97881000	Flanking Active TSS	Pancreas	Pancrea
31	chr7:97880200-97881000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr7:97880200-97881000	Flanking Active TSS	A549	lung
33	chr7:97880200-97881000	Flanking Active TSS	K562	blood
34	chr7:97880200-97881200	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr7:97880200-97881200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:97880200-97881200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:97880200-97881200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr7:97880200-97881200	Flanking Active TSS	Hela-S3	cervix
39	chr7:97880200-97881400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:97880200-97881400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:97880200-97881400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:97880200-97881400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr7:97880200-97881400	Flanking Active TSS	Colonic Mucosa	Colon
44	chr7:97880200-97881400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr7:97880200-97881400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr7:97880200-97882000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr7:97880200-97882600	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr7:97880200-97882600	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr7:97880400-97880800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:97880400-97880800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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