Variant report

Variant	rs1076392
Chromosome Location	chr17:59493008-59493009
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	NRF1	chr17:59492542-59494977	SK-N-SH	brain:	n/a	chr17:59494254-59494263 chr17:59494253-59494264 chr17:59494254-59494265 chr17:59494254-59494268 chr17:59494251-59494265
2	GATA3	chr17:59491635-59494906	MCF-7	breast:	n/a	chr17:59491884-59491894 chr17:59492575-59492585
3	TEAD4	chr17:59484276-59495088	A549	lung:	n/a	n/a
4	POLR2A	chr17:59492545-59493300	HepG2	liver:	n/a	n/a
5	MAX	chr17:59484138-59500997	MCF-7	breast:	n/a	chr17:59495541-59495552 chr17:59492978-59492987 chr17:59491213-59491223 chr17:59491485-59491495 chr17:59495570-59495581 chr17:59488910-59488926
6	POLR2A	chr17:59492889-59493166	ProgFib	skin:	n/a	n/a
7	POLR2A	chr17:59493007-59493089	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr17:59492880-59493030	GM12866	blood:	n/a	n/a
9	RAD21	chr17:59491533-59495532	SK-N-SH	brain:	n/a	chr17:59494032-59494042 chr17:59494302-59494312 chr17:59494404-59494413
10	HDAC2	chr17:59482687-59495676	MCF-7	breast:	n/a	chr17:59487075-59487094 chr17:59495598-59495612 chr17:59495596-59495610 chr17:59495599-59495613 chr17:59495595-59495609 chr17:59494256-59494265 chr17:59492574-59492588
11	SMC3	chr17:59492883-59495084	SK-N-SH	brain:	n/a	chr17:59494032-59494042

No.	Distal block	Cell Line	Cell type
1	chr17:59492509..59494199-chr20:55685011..55687223,2	MCF-7	breast:
2	chr17:59492663..59495167-chr9:114775467..114777487,2	MCF-7	breast:
3	chr17:59492196..59494427-chr17:59818086..59820888,2	MCF-7	breast:
4	chr17:59492296..59494354-chr2:239997406..240000023,2	MCF-7	breast:
5	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
6	chr17:59483268..59486484-chr17:59491273..59493392,3	K562	blood:
7	chr17:59492061..59493575-chr2:55052880..55054380,2	MCF-7	breast:
8	chr17:59492572..59494838-chr19:47729176..47730869,2	MCF-7	breast:
9	chr17:59491684..59493481-chr7:20368667..20370695,2	MCF-7	breast:
10	chr17:59094691..59097620-chr17:59491568..59493093,2	MCF-7	breast:
11	chr17:59490811..59493565-chr9:80089592..80091840,2	MCF-7	breast:
12	chr17:59490397..59493114-chr17:60868555..60870113,2	MCF-7	breast:
13	chr17:59491612..59493319-chr17:59927400..59929944,2	MCF-7	breast:
14	chr17:59486789..59493376-chr20:46130669..46135131,5	MCF-7	breast:
15	chr17:59492727..59496859-chr17:59625979..59629778,204	MCF-7	breast:
16	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
17	chr17:59492287..59493196-chr17:59629241..59629768,2	MCF-7	breast:
18	chr17:59492520..59494967-chr20:48598399..48600896,2	MCF-7	breast:
19	chr17:57919319..57922572-chr17:59492471..59494276,4	MCF-7	breast:
20	chr17:59492385..59494445-chr20:52930380..52933375,2	MCF-7	breast:
21	chr17:59491548..59493731-chr17:64460964..64463383,2	MCF-7	breast:
22	chr17:59490904..59493858-chr5:81572794..81575325,2	MCF-7	breast:
23	chr17:59486918..59494123-chr20:45984608..45990861,17	MCF-7	breast:
24	chr17:59491669..59494227-chr20:52486642..52489549,2	MCF-7	breast:
25	chr17:59492965..59494895-chr20:48757596..48759628,2	MCF-7	breast:
26	chr17:59491155..59493434-chr3:64672960..64675893,2	MCF-7	breast:
27	chr17:59492469..59495973-chr17:73772457..73777286,6	MCF-7	breast:
28	chr17:57968948..57972099-chr17:59491363..59493598,3	MCF-7	breast:
29	chr17:56735008..56738004-chr17:59488690..59493037,7	MCF-7	breast:
30	chr17:59477614..59480585-chr17:59492115..59493816,2	K562	blood:
31	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267280	TF binding region
ENSG00000105327	Chromatin interaction
ENSG00000163638	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000205464	Chromatin interaction
ENSG00000186468	Chromatin interaction
ENSG00000105855	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000265134	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000132475	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2079795	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109019	0.85[CHD][hapmap];0.86[GIH][hapmap]
rs2286528	0.81[JPT][hapmap]
rs7214743	0.95[CEU][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs740755	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs757608	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs758598	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064243	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs882367	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9892365	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9905385	1.00[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9907379	0.90[CHD][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
5	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
6	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
7	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
8	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases
9	nsv908671	chr17:59475888-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
10	nsv908672	chr17:59476062-59494574	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
11	nsv519931	chr17:59491281-59514461	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1076392	TBX4	cis	cerebellum	SCAN
rs1076392	MRC2	cis	cerebellum	SCAN
rs1076392	NACA2	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59490200-59493800	Weak transcription	K562	blood
2	chr17:59490400-59493600	Weak transcription	HSMMtube	muscle
3	chr17:59490400-59493800	Weak transcription	Liver	Liver
4	chr17:59490600-59493800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr17:59490600-59493800	Weak transcription	Brain Angular Gyrus	brain
6	chr17:59490600-59493800	Weak transcription	Gastric	stomach
7	chr17:59490600-59494000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr17:59490600-59494000	Weak transcription	Esophagus	oesophagus
9	chr17:59490600-59494000	Weak transcription	HMEC	breast
10	chr17:59490600-59494200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr17:59490600-59494200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr17:59490800-59493200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:59490800-59494000	Weak transcription	Brain Anterior Caudate	brain
14	chr17:59490800-59494000	Weak transcription	Brain Substantia Nigra	brain
15	chr17:59490800-59494000	Weak transcription	Pancreas	Pancrea
16	chr17:59491000-59493200	Weak transcription	NH-A	brain
17	chr17:59491000-59493600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr17:59491000-59493800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:59491000-59493800	Enhancers	Adipose Nuclei	Adipose
20	chr17:59491000-59493800	Weak transcription	Fetal Heart	heart
21	chr17:59491000-59493800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr17:59491000-59493800	Enhancers	NHDF-Ad	bronchial
23	chr17:59491000-59494000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:59491000-59494000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr17:59491000-59494000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:59491000-59494000	Bivalent Enhancer	Fetal Stomach	stomach
27	chr17:59491000-59494600	Enhancers	Lung	lung
28	chr17:59491000-59495600	Enhancers	Placenta	Placenta
29	chr17:59491000-59504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:59491200-59493800	Enhancers	Osteobl	bone
31	chr17:59491200-59494000	Weak transcription	Fetal Kidney	kidney
32	chr17:59491400-59493200	Enhancers	Spleen	Spleen
33	chr17:59491800-59494600	Enhancers	NHLF	lung
34	chr17:59492000-59493200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr17:59492000-59493600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr17:59492000-59493600	Enhancers	Fetal Lung	lung
37	chr17:59492000-59494000	Weak transcription	Hela-S3	cervix
38	chr17:59492200-59493200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr17:59492200-59493800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:59492200-59493800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr17:59492200-59493800	Weak transcription	Right Atrium	heart
42	chr17:59492200-59494000	Weak transcription	Left Ventricle	heart
43	chr17:59492200-59494200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr17:59492400-59493800	Enhancers	Fetal Muscle Leg	muscle
45	chr17:59492400-59494000	Weak transcription	Right Ventricle	heart
46	chr17:59492400-59494000	Enhancers	HepG2	liver
47	chr17:59492400-59494200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr17:59492600-59493800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr17:59492600-59493800	Weak transcription	Ovary	ovary
50	chr17:59492600-59493800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links