Variant report

Variant	rs12904
Chromosome Location	chr1:155106697-155106698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155106405-155108990	Hela-S3	cervix:	n/a	n/a
2	HCFC1	chr1:155106158-155109044	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:155105642-155108644	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:155105844-155108967	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:155106105-155108979	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:155106688-155107102	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr1:155106188-155109004	MCF-7	breast:	n/a	chr1:155108662-155108672 chr1:155108649-155108659
8	POLR2A	chr1:155105587-155108949	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:155105878-155108823	A549	lung:	n/a	n/a
10	POLR2A	chr1:155105749-155108991	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:155106270-155109026	Hela-S3	cervix:	n/a	n/a
12	MAX	chr1:155106590-155109035	A549	lung:	n/a	chr1:155108662-155108672 chr1:155108649-155108659
13	POLR2A	chr1:155104784-155113272	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:155105627-155108964	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:155106069-155111034	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr1:155106244-155107192	HepG2	liver:	n/a	n/a
17	MXI1	chr1:155106144-155108888	HepG2	liver:	n/a	n/a
18	NR2F2	chr1:155105902-155109005	HepG2	liver:	n/a	chr1:155106405-155106420
19	NR2F2	chr1:155105970-155106799	MCF-7	breast:	n/a	chr1:155106405-155106420
20	GATA3	chr1:155106097-155106734	MCF-7	breast:	n/a	n/a
21	HEY1	chr1:155105595-155109009	HepG2	liver:	n/a	chr1:155108266-155108281
22	POLR2A	chr1:155105850-155108982	HepG2	liver:	n/a	n/a
23	NR2F2	chr1:155106119-155106753	HepG2	liver:	n/a	chr1:155106405-155106420

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154192341..154194171-chr1:155106625..155108137,2	MCF-7	breast:
2	chr1:155049589..155073019-chr1:155085330..155115362,149	MCF-7	breast:
3	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
4	chr1:155106609..155109409-chr1:155161242..155164268,3	MCF-7	breast:
5	chr1:150120710..150123122-chr1:155106674..155108306,2	MCF-7	breast:
6	chr1:155106358..155107894-chr1:155178514..155180234,2	K562	blood:
7	chr1:155034568..155037098-chr1:155106619..155109204,2	MCF-7	breast:
8	chr1:155052471..155058946-chr1:155106509..155113930,10	K562	blood:
9	chr1:155106208..155110263-chr1:155170377..155171955,3	K562	blood:
10	chr1:155105664..155110180-chr1:155143584..155151850,15	MCF-7	breast:
11	chr1:155106165..155110704-chr1:155161873..155165835,8	K562	blood:
12	chr1:155105295..155110704-chr1:155161873..155165835,7	K562	blood:
13	chr1:155106166..155110794-chr1:155110873..155115238,14	K562	blood:
14	chr1:154973938..154977904-chr1:155106692..155109973,4	MCF-7	breast:
15	chr1:155106515..155109128-chr1:155196131..155198130,2	K562	blood:
16	chr1:155066527..155067288-chr1:155106043..155106834,2	MCF-7	breast:
17	chr1:154944220..154948259-chr1:155103576..155107473,5	MCF-7	breast:

No data

Variant related genes	Relation type
SLC50A1	TF binding region
ENSG00000163462	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000143590	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000179085	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000163463	Chromatin interaction
ENSG00000023902	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1001848	0.85[JPT][hapmap]
rs10157801	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908454	0.85[JPT][hapmap]
rs10908455	0.85[JPT][hapmap]
rs10908456	0.85[JPT][hapmap]
rs10908458	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264306	0.85[JPT][hapmap]
rs11264314	0.82[JPT][hapmap]
rs11264319	0.85[JPT][hapmap]
rs11264327	0.83[EUR][1000 genomes]
rs11264329	0.85[JPT][hapmap]
rs11264333	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264337	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs11264338	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs11264339	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs11799962	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11807418	0.81[EUR][1000 genomes]
rs12025371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12028043	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12040970	0.85[JPT][hapmap]
rs12124306	0.85[EUR][1000 genomes]
rs12127609	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12137164	0.81[EUR][1000 genomes]
rs12145362	0.84[CEU][hapmap];0.80[GIH][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs1462855	0.85[JPT][hapmap]
rs1870939	0.85[JPT][hapmap]
rs2066981	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs2306124	0.85[JPT][hapmap]
rs34257409	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3765087	0.85[JPT][hapmap]
rs3766916	0.85[JPT][hapmap]
rs3814316	0.85[CHB][hapmap]
rs4072037	0.92[CHB][hapmap];0.96[CHD][hapmap]
rs4246529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4276913	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4390169	1.00[ASN][1000 genomes]
rs4421576	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4460629	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4845407	0.85[JPT][hapmap]
rs4845408	0.85[JPT][hapmap]
rs4971052	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4971054	0.82[EUR][1000 genomes]
rs4971059	0.85[CHB][hapmap];0.81[CHD][hapmap];0.81[AMR][1000 genomes]
rs4971066	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4971073	0.92[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971076	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971079	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4971085	1.00[CHB][hapmap]
rs4971088	1.00[CHB][hapmap]
rs4971093	0.84[AMR][1000 genomes]
rs6427158	0.85[JPT][hapmap]
rs6665822	0.85[JPT][hapmap]
rs6676150	0.89[ASN][1000 genomes]
rs6693477	0.85[JPT][hapmap]
rs7364524	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7365544	0.85[JPT][hapmap]
rs7366138	0.82[EUR][1000 genomes]
rs7367207	0.85[JPT][hapmap]
rs7367897	0.85[JPT][hapmap]
rs7368345	0.85[JPT][hapmap]
rs7534162	0.85[JPT][hapmap]
rs7548955	0.82[JPT][hapmap]
rs7556304	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs914615	0.83[CHB][hapmap]
rs9297	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
6	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
7	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12904	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155102400-155106800	Weak transcription	Dnd41	blood
2	chr1:155102400-155107000	Weak transcription	HSMM	muscle
3	chr1:155102400-155107400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:155102400-155107400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:155102600-155107400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:155102800-155107000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr1:155102800-155107000	Weak transcription	NH-A	brain
8	chr1:155102800-155107200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:155102800-155107400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:155103000-155107200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:155103000-155107400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:155103200-155106800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:155103400-155107000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:155103400-155107000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:155103400-155107200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:155103600-155106800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:155103600-155107000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:155103600-155107000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:155103800-155107000	Strong transcription	Fetal Stomach	stomach
20	chr1:155103800-155107200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:155103800-155107200	Weak transcription	Fetal Brain Female	brain
22	chr1:155103800-155107200	Strong transcription	Thymus	Thymus
23	chr1:155103800-155107400	Genic enhancers	Fetal Intestine Large	intestine
24	chr1:155104000-155106800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:155104000-155106800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:155104000-155107200	Genic enhancers	Fetal Intestine Small	intestine
27	chr1:155104000-155107400	Genic enhancers	HUVEC	blood vessel
28	chr1:155104200-155106800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:155104200-155107200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:155104200-155107400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:155104200-155107400	Weak transcription	Aorta	Aorta
32	chr1:155104400-155106800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:155104400-155107000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:155104400-155107000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:155104400-155107400	Genic enhancers	Left Ventricle	heart
36	chr1:155104600-155106800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:155104600-155106800	Genic enhancers	Right Ventricle	heart
38	chr1:155104600-155106800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr1:155104600-155107000	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr1:155104600-155107000	Weak transcription	Fetal Lung	lung
41	chr1:155104600-155107000	Weak transcription	Right Atrium	heart
42	chr1:155104600-155107200	Weak transcription	Fetal Kidney	kidney
43	chr1:155104600-155107400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:155104600-155107400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:155104600-155107400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:155105000-155106800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:155105400-155106800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:155105400-155107000	Genic enhancers	Brain Hippocampus Middle	brain
49	chr1:155105600-155106800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:155105600-155106800	Strong transcription	Brain Inferior Temporal Lobe	brain

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