Variant report

Variant	rs4407796
Chromosome Location	chr7:140098605-140098606
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	USF1	chr7:140098092-140098620	A549	lung:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
2	MXI1	chr7:140097379-140098656	IMR90	lung:	n/a	n/a
3	ETS1	chr7:140097834-140098654	K562	blood:	n/a	chr7:140098167-140098178 chr7:140098368-140098381 chr7:140098369-140098382 chr7:140098370-140098377
4	ZNF384	chr7:140098216-140098699	GM12878	blood:	n/a	n/a
5	MXI1	chr7:140096999-140098830	SK-N-SH	brain:	n/a	n/a
6	ATF3	chr7:140098141-140098605	HepG2	liver:	n/a	n/a
7	MAX	chr7:140097437-140098654	SK-N-SH	brain:	n/a	chr7:140098384-140098393
8	SREBP1	chr7:140097966-140098831	GM12878	blood:	n/a	n/a
9	EGR1	chr7:140097807-140098725	HCT-116	colon:	n/a	chr7:140098164-140098178 chr7:140098165-140098178 chr7:140098166-140098175 chr7:140098164-140098179 chr7:140098357-140098381 chr7:140098165-140098178 chr7:140098165-140098175 chr7:140098283-140098297 chr7:140098165-140098178 chr7:140098165-140098178
10	GABPA	chr7:140098012-140098681	SK-N-SH	brain:	n/a	chr7:140098205-140098214
11	TAF1	chr7:140097692-140098616	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr7:140097587-140098620	MCF10A-Er-Src	breast:	n/a	n/a
13	SIN3AK20	chr7:140097967-140098762	MCF-7	breast:	n/a	n/a
14	USF1	chr7:140097883-140098712	HCT-116	colon:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
15	EP300	chr7:140098221-140098612	K562	blood:	n/a	chr7:140098401-140098410 chr7:140098502-140098516
16	E2F6	chr7:140097683-140098905	K562	blood:	n/a	chr7:140098401-140098410
17	STAT5A	chr7:140098053-140098626	K562	blood:	n/a	n/a
18	TCF12	chr7:140097958-140098639	ECC-1	luminal epithelium:	n/a	n/a
19	MAX	chr7:140097799-140098653	HepG2	liver:	n/a	chr7:140098384-140098393
20	USF1	chr7:140098055-140098614	A549	lung:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
21	USF1	chr7:140098002-140098661	K562	blood:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
22	RCOR1	chr7:140098389-140098630	K562	blood:	n/a	n/a
23	JUN	chr7:140097346-140099101	K562	blood:	n/a	chr7:140098104-140098113
24	USF1	chr7:140098084-140098702	SK-N-SH	brain:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
25	RCOR1	chr7:140097627-140098605	K562	blood:	n/a	n/a
26	USF1	chr7:140098044-140098624	H1-hESC	embryonic stem cell:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
27	MAX	chr7:140097576-140098760	HCT-116	colon:	n/a	chr7:140098384-140098393
28	ZNF143	chr7:140097541-140098636	K562	blood:	n/a	chr7:140098118-140098127 chr7:140098116-140098134 chr7:140098045-140098063 chr7:140098357-140098376 chr7:140098358-140098373 chr7:140098369-140098378 chr7:140098371-140098380 chr7:140098362-140098380
29	MAX	chr7:140098036-140098663	ECC-1	luminal epithelium:	n/a	chr7:140098384-140098393
30	HDAC2	chr7:140097951-140098611	MCF-7	breast:	n/a	chr7:140098501-140098515
31	TCF12	chr7:140097282-140098705	SK-N-SH	brain:	n/a	n/a
32	ZMIZ1	chr7:140098108-140098643	K562	blood:	n/a	n/a
33	SIX5	chr7:140098123-140098621	GM12878	blood:	n/a	chr7:140098369-140098378 chr7:140098371-140098380
34	HCFC1	chr7:140097577-140098774	K562	blood:	n/a	n/a
35	USF1	chr7:140098063-140098615	ECC-1	luminal epithelium:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
36	ETS1	chr7:140098018-140098660	A549	lung:	n/a	chr7:140098167-140098178 chr7:140098368-140098381 chr7:140098369-140098382 chr7:140098370-140098377
37	USF2	chr7:140098148-140098628	GM12878	blood:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
38	MAX	chr7:140097736-140098615	H1-hESC	embryonic stem cell:	n/a	chr7:140098384-140098393
39	POLR2A	chr7:140098026-140098623	HCT-116	colon:	n/a	n/a
40	GABPA	chr7:140097975-140098709	MCF-7	breast:	n/a	chr7:140098205-140098214
41	SIX5	chr7:140097969-140098700	A549	lung:	n/a	chr7:140098369-140098378 chr7:140098371-140098380 chr7:140098118-140098127
42	TBL1XR1	chr7:140098271-140098638	K562	blood:	n/a	n/a
43	ZNF263	chr7:140098233-140098625	HEK293-T-REx	kidney:	n/a	chr7:140098408-140098429
44	USF1	chr7:140097986-140098796	HCT-116	colon:	n/a	chr7:140098388-140098404 chr7:140098167-140098183 chr7:140098337-140098348
45	MAX	chr7:140097677-140098611	MCF-7	breast:	n/a	chr7:140098384-140098393
46	EGR1	chr7:140097828-140098677	HCT-116	colon:	n/a	chr7:140098164-140098178 chr7:140098165-140098178 chr7:140098166-140098175 chr7:140098164-140098179 chr7:140098357-140098381 chr7:140098165-140098178 chr7:140098165-140098175 chr7:140098283-140098297 chr7:140098165-140098178 chr7:140098165-140098178
47	ZNF384	chr7:140098142-140098979	K562	blood:	n/a	n/a
48	HCFC1	chr7:140097337-140098819	Hela-S3	cervix:	n/a	n/a
49	NR2F2	chr7:140097146-140098965	K562	blood:	n/a	n/a
50	MAX	chr7:140098022-140098624	MCF-7	breast:	n/a	chr7:140098384-140098393

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:140098579-140098629	HAEpiC	amniotic membrane:	n/a
2	chr7:140098579-140098629	GM12878	blood:	n/a
3	chr7:140098579-140098629	GM12891	blood:	n/a
4	chr7:140098579-140098629	NHBE	bronchial:	n/a
5	chr7:140098579-140098629	Hela-S3	cervix:	n/a
6	chr7:140098579-140098629	AG04449	skin:	fetal
7	chr7:140098579-140098629	HRE	kidney:	n/a
8	chr7:140098579-140098629	PANC-1	pancreas:	n/a
9	chr7:140098579-140098629	SK-N-MC	brain:	n/a
10	chr7:140098579-140098629	NB4	blood:	n/a
11	chr7:140098579-140098629	Hepatocyte	liver:	n/a
12	chr7:140098579-140098629	Jurkat	blood:	n/a
13	chr7:140098579-140098629	HepG2	liver:	n/a
14	chr7:140098579-140098629	BE2_C	brain:	n/a
15	chr7:140098579-140098629	ECC-1	luminal epithelium:	n/a
16	chr7:140098579-140098629	HCF	heart:	n/a
17	chr7:140098579-140098629	HEK293	kidney:	embryo
18	chr7:140098579-140098629	HUVEC	blood vessel:	n/a
19	chr7:140098579-140098629	CMK	blood:	n/a
20	chr7:140098579-140098629	LNCaP	prostate:	n/a
21	chr7:140098579-140098629	SK-N-SH	brain:	n/a
22	chr7:140098579-140098629	PFSK-1	brain:	n/a
23	chr7:140098579-140098629	HEEpiC	esophagus:	n/a
24	chr7:140098579-140098629	GM19239	blood:	n/a
25	chr7:140098579-140098629	IMR90	lung:	fetal
26	chr7:140098579-140098629	BJ	skin:	n/a
27	chr7:140098579-140098629	PrEC	prostate:	n/a
28	chr7:140098579-140098629	U87	brain:	n/a
29	chr7:140098579-140098629	NH-A	brain:	n/a
30	chr7:140098579-140098629	NT2-D1	testis:	n/a
31	chr7:140098579-140098629	AG10803	skin:	n/a
32	chr7:140098579-140098629	MCF10A-Er-Src	breast:	n/a
33	chr7:140098579-140098629	ovcar-3	ovarian:	n/a
34	chr7:140098579-140098629	RPTEC	kidney:	n/a
35	chr7:140098579-140098629	HIPEpiC	eye:	n/a
36	chr7:140098579-140098629	HMEC	breast:	n/a
37	chr7:140098579-140098629	HL-60	blood:	n/a
38	chr7:140098579-140098629	HCPEpiC	choroid plexus:	n/a
39	chr7:140098579-140098629	HPAEpiC	pulmonary alveolar:	n/a
40	chr7:140098579-140098629	K562	blood:	n/a
41	chr7:140098579-140098629	AG09309	skin:	n/a
42	chr7:140098579-140098629	H1-hESC	embryonic stem cell:	embryo
43	chr7:140098579-140098629	AG09319	gingival:	n/a
44	chr7:140098579-140098629	MCF-7	breast:	n/a
45	chr7:140098579-140098629	A549	lung:	n/a
46	chr7:140098579-140098629	HRCEpiC	kidney:	n/a
47	chr7:140098579-140098629	HNPCEpiC	eye:	n/a
48	chr7:140098579-140098629	SKMC	muscle:	n/a
49	chr7:140098579-140098629	HRPEpiC	eye:	n/a
50	chr7:140098579-140098629	SAEC	small airway:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:140097102..140100754-chr7:140100879..140105218,4	MCF-7	breast:
2	chr13:52026703..52027221-chr7:140097973..140098689,2	HCT-116	colon:
3	chr7:140096834..140099391-chr7:140178947..140180902,2	K562	blood:
4	chr7:139875282..139878278-chr7:140096376..140098840,2	MCF-7	breast:
5	chr7:140075069..140077735-chr7:140096588..140099526,2	MCF-7	breast:

Variant related genes	Relation type
SLC37A3	TF binding region
SLC37A3	CpG island
ENSG00000238868	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000260231	Chromatin interaction
ENSG00000006459	Chromatin interaction
ENSG00000133606	Chromatin interaction
ENSG00000146955	Chromatin interaction
ENSG00000157800	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10256523	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs4407796	OR9A2	cis	cerebellum	SCAN
rs4407796	SLC37A3	cis	parietal	SCAN
rs4407796	ZC3HAV1L	cis	parietal	SCAN
rs4407796	CREB3L2	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140096000-140098800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:140096800-140098800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:140097200-140098800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr7:140097400-140098800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:140097400-140098800	Active TSS	Brain Cingulate Gyrus	brain
6	chr7:140097400-140098800	Active TSS	Fetal Intestine Small	intestine
7	chr7:140097400-140098800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr7:140097400-140099000	Active TSS	Fetal Kidney	kidney
9	chr7:140097800-140098800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr7:140097800-140099000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:140098000-140098800	Active TSS	HepG2	liver
12	chr7:140098000-140103800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr7:140098200-140098800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:140098400-140098800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr7:140098400-140098800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr7:140098400-140098800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr7:140098400-140098800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:140098400-140098800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:140098400-140098800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:140098400-140098800	Enhancers	Fetal Thymus	thymus
21	chr7:140098400-140098800	Weak transcription	Gastric	stomach
22	chr7:140098400-140098800	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr7:140098400-140098800	Flanking Active TSS	Dnd41	blood
24	chr7:140098400-140099000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr7:140098400-140103400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr7:140098400-140103600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:140098400-140103600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:140098400-140103600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:140098400-140103600	Weak transcription	Small Intestine	intestine
30	chr7:140098400-140103600	Weak transcription	Spleen	Spleen
31	chr7:140098600-140098800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr7:140098600-140098800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr7:140098600-140098800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr7:140098600-140098800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:140098600-140098800	Enhancers	Primary B cells from peripheral blood	blood
36	chr7:140098600-140098800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr7:140098600-140098800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:140098600-140098800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:140098600-140098800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:140098600-140098800	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr7:140098600-140098800	Enhancers	Brain Anterior Caudate	brain
42	chr7:140098600-140098800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr7:140098600-140098800	Flanking Active TSS	Colonic Mucosa	Colon
44	chr7:140098600-140098800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr7:140098600-140098800	Enhancers	Fetal Brain Male	brain
46	chr7:140098600-140098800	Flanking Active TSS	Fetal Brain Female	brain
47	chr7:140098600-140098800	Enhancers	Fetal Muscle Trunk	muscle
48	chr7:140098600-140098800	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr7:140098600-140098800	Enhancers	Lung	lung
50	chr7:140098600-140098800	Flanking Active TSS	Pancreas	Pancrea

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