Variant report

Variant	rs17030475
Chromosome Location	chr1:113086626-113086627
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	SMC3	chr1:113086602-113086965	Hela-S3	cervix:	n/a	n/a
2	JUND	chr1:113086534-113087782	Hela-S3	cervix:	n/a	chr1:113086849-113086860
3	TCF12	chr1:113086557-113087196	SK-N-SH	brain:	n/a	chr1:113086588-113086597
4	STAT3	chr1:113086603-113086995	MCF10A-Er-Src	breast:	n/a	chr1:113086814-113086822
5	GABPA	chr1:113086585-113087084	SK-N-SH	brain:	n/a	n/a
6	SP1	chr1:113086558-113087073	A549	lung:	n/a	n/a
7	FOSL2	chr1:113086518-113087206	SK-N-SH	brain:	n/a	n/a
8	STAT3	chr1:113086501-113086911	MCF10A-Er-Src	breast:	n/a	chr1:113086814-113086822
9	GATA3	chr1:113086502-113087165	A549	lung:	n/a	chr1:113086623-113086639
10	POLR2A	chr1:113086586-113087025	HCT-116	colon:	n/a	n/a
11	POLR2A	chr1:113086547-113087230	U87	brain:	n/a	n/a
12	NFIC	chr1:113086437-113087180	SK-N-SH	brain:	n/a	n/a
13	ATF3	chr1:113086526-113086965	HCT-116	colon:	n/a	n/a
14	CEBPB	chr1:113086616-113087145	HCT-116	colon:	n/a	n/a
15	BRCA1	chr1:113086593-113087798	Hela-S3	cervix:	n/a	n/a
16	EP300	chr1:113086561-113087178	ECC-1	luminal epithelium:	n/a	chr1:113086824-113086832
17	TEAD4	chr1:113086517-113087178	SK-N-SH	brain:	n/a	n/a
18	STAT3	chr1:113086578-113087113	MCF10A-Er-Src	breast:	n/a	chr1:113086814-113086822
19	JUND	chr1:113086516-113087188	HCT-116	colon:	n/a	chr1:113086849-113086860
20	FOSL2	chr1:113086609-113086985	A549	lung:	n/a	n/a
21	TEAD4	chr1:113086575-113087142	ECC-1	luminal epithelium:	n/a	n/a
22	CBX3	chr1:113086512-113087080	HCT-116	colon:	n/a	n/a
23	TCF12	chr1:113086593-113087100	A549	lung:	n/a	n/a
24	POLR2A	chr1:113086589-113087044	SK-N-SH	brain:	n/a	n/a
25	FOSL1	chr1:113086484-113087104	HCT-116	colon:	n/a	n/a
26	RFX5	chr1:113086602-113087828	Hela-S3	cervix:	n/a	n/a
27	MEF2A	chr1:113086462-113087189	SK-N-SH	brain:	n/a	n/a
28	MEF2A	chr1:113086544-113087075	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr1:113086557-113087027	U87	brain:	n/a	n/a
30	EP300	chr1:113086428-113087806	SK-N-SH	brain:	n/a	chr1:113086824-113086832
31	RXRA	chr1:113086562-113087172	SK-N-SH	brain:	n/a	chr1:113086851-113086860 chr1:113087139-113087153 chr1:113086871-113086880
32	JUND	chr1:113086502-113087224	HCT-116	colon:	n/a	chr1:113086849-113086860
33	CEBPB	chr1:113086622-113087775	Hela-S3	cervix:	n/a	chr1:113087676-113087693
34	GATA3	chr1:113086520-113087215	SK-N-SH	brain:	n/a	chr1:113086623-113086639
35	MEF2A	chr1:113086533-113086993	K562	blood:	n/a	n/a
36	TBP	chr1:113086606-113087227	Hela-S3	cervix:	n/a	n/a
37	GABPA	chr1:113086505-113087122	SK-N-SH	brain:	n/a	n/a
38	TEAD4	chr1:113086509-113087076	HCT-116	colon:	n/a	n/a
39	FOSL1	chr1:113086426-113087288	HCT-116	colon:	n/a	n/a
40	TEAD4	chr1:113086505-113087122	A549	lung:	n/a	n/a
41	FOSL2	chr1:113086512-113087220	A549	lung:	n/a	n/a
42	FOS	chr1:113086621-113087005	Hela-S3	cervix:	n/a	chr1:113086849-113086860
43	POLR2A	chr1:113086475-113087190	HUVEC	blood vessel:	n/a	n/a
44	CEBPB	chr1:113086439-113087251	HCT-116	colon:	n/a	n/a
45	FOS	chr1:113086618-113087192	HUVEC	blood vessel:	n/a	chr1:113086849-113086860
46	TEAD4	chr1:113086581-113087002	A549	lung:	n/a	n/a
47	ELF1	chr1:113086586-113087104	SK-N-SH	brain:	n/a	n/a
48	GABPA	chr1:113086613-113087096	A549	lung:	n/a	n/a
49	RXRA	chr1:113086522-113087158	SK-N-SH	brain:	n/a	chr1:113086851-113086860 chr1:113087139-113087153 chr1:113086871-113086880
50	PBX3	chr1:113086485-113087127	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ST7L	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10399919	0.90[AFR][1000 genomes]
rs11102490	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102492	1.00[AMR][1000 genomes]
rs11102493	1.00[MEX][hapmap]
rs11102500	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102511	0.86[AFR][1000 genomes]
rs11102519	0.81[AFR][1000 genomes]
rs1175632	1.00[MEX][hapmap]
rs1175640	1.00[MEX][hapmap]
rs1175642	1.00[MEX][hapmap]
rs12060267	1.00[AFR][1000 genomes]
rs12069022	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069740	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12073750	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes]
rs12074157	0.81[AFR][1000 genomes]
rs12077330	0.90[AFR][1000 genomes]
rs12080006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082350	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12085734	1.00[MEX][hapmap]
rs12087862	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs12091635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094504	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095563	0.81[AFR][1000 genomes]
rs17030350	1.00[MEX][hapmap]
rs17030446	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030451	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030455	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030592	0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs1936047	1.00[MEX][hapmap]
rs4424506	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs58634778	0.90[AFR][1000 genomes]
rs59324334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.86[AFR][1000 genomes]
rs72984503	0.90[AFR][1000 genomes]
rs72986505	0.81[AFR][1000 genomes]
rs72993070	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72993072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7542272	1.00[MEX][hapmap]
rs9919308	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:113058800-113119400	Weak transcription	HepG2	liver
3	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
4	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
5	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
9	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
10	chr1:113066000-113088800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:113066200-113114400	Weak transcription	Dnd41	blood
14	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
15	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr1:113068000-113089600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
18	chr1:113068800-113087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:113070400-113095400	Weak transcription	Gastric	stomach
20	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
21	chr1:113070600-113088200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:113070600-113117800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
28	chr1:113071200-113090600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:113072000-113114400	Weak transcription	Brain Anterior Caudate	brain
30	chr1:113072600-113087000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:113076400-113115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:113078800-113090200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:113079600-113087000	Weak transcription	HSMMtube	muscle
34	chr1:113080200-113117800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:113080800-113117400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
37	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:113082000-113106600	Weak transcription	Fetal Kidney	kidney
40	chr1:113082000-113116000	Weak transcription	Left Ventricle	heart
41	chr1:113082000-113117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:113082200-113118000	Weak transcription	Lung	lung
43	chr1:113083000-113088200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
45	chr1:113083400-113087000	Weak transcription	Adipose Nuclei	Adipose
46	chr1:113083400-113087000	Weak transcription	NHLF	lung
47	chr1:113083600-113088200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:113083600-113091000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:113083600-113111600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:113083600-113114400	Weak transcription	Fetal Brain Female	brain

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