Variant report

Variant	rs7517566
Chromosome Location	chr1:150850035-150850036
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr1:150847697-150850134	SK-N-SH	brain:	n/a	n/a
2	NR2F2	chr1:150848371-150850122	MCF-7	breast:	n/a	n/a
3	STAT3	chr1:150849901-150850110	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr1:150849874-150850290	K562	blood:	n/a	chr1:150850154-150850165
5	KAP1	chr1:150849161-150850098	HEK293	kidney:	n/a	n/a
6	GTF3C2	chr1:150849336-150850044	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr1:150848529-150850066	IMR90	lung:	n/a	n/a
8	CTCF	chr1:150849940-150850090	NHLF	lung:	n/a	n/a
9	TCF12	chr1:150848407-150850083	A549	lung:	n/a	chr1:150849981-150849988 chr1:150848802-150848812

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150549744..150554023-chr1:150847608..150851573,5	K562	blood:
2	chr1:150848716..150851402-chr1:150897221..150900291,3	MCF-7	breast:
3	chr1:150847931..150851587-chr1:150853004..150856091,6	K562	blood:
4	chr1:150849390..150851277-chr1:150877417..150879109,2	MCF-7	breast:
5	chr1:150846965..150851829-chr1:150851958..150856513,6	MCF-7	breast:
6	chr1:150549206..150551464-chr1:150847559..150850045,2	K562	blood:
7	chr1:150847356..150848927-chr1:150849575..150851202,2	K562	blood:
8	chr1:150847391..150850807-chr1:150896212..150900555,5	MCF-7	breast:
9	chr1:150847696..150850504-chr1:150946094..150948149,2	K562	blood:
10	chr1:150849097..150850809-chr1:150979255..150981896,2	MCF-7	breast:
11	chr1:150846616..150850276-chr1:150942456..150948926,7	MCF-7	breast:
12	chr1:150336081..150337653-chr1:150849061..150850708,2	K562	blood:
13	chr1:150846958..150850554-chr1:150897225..150899118,3	K562	blood:
14	chr1:150848386..150850942-chr1:150853921..150858032,4	K562	blood:

No data

Variant related genes	Relation type
ARNT	TF binding region
ENSG00000231073	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000224800	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000212512	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10788795	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10888396	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204714	0.85[EUR][1000 genomes]
rs11204715	0.85[EUR][1000 genomes]
rs11204727	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs11576175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs12728254	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1415146	0.85[YRI][hapmap]
rs16832604	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs16840074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1811698	0.84[ASN][1000 genomes]
rs2134688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs267727	0.85[YRI][hapmap]
rs267736	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes]
rs3738483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754210	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs3768017	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820541	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820543	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4379678	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs533928	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61817598	0.82[EUR][1000 genomes]
rs61817600	0.88[EUR][1000 genomes]
rs61817649	0.91[EUR][1000 genomes]
rs6661100	0.88[EUR][1000 genomes]
rs6671703	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679701	0.92[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6688248	0.91[EUR][1000 genomes]
rs6692277	0.88[EUR][1000 genomes]
rs6696167	0.88[EUR][1000 genomes]
rs72704624	0.88[EUR][1000 genomes]
rs7529204	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7535848	0.91[EUR][1000 genomes]
rs7535975	0.85[EUR][1000 genomes]
rs771204	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150847000-150850200	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr1:150847400-150850200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr1:150847400-150850200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:150847600-150850200	Active TSS	A549	lung
5	chr1:150849200-150852800	Weak transcription	NHLF	lung
6	chr1:150849600-150850200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:150849600-150850200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:150849600-150850800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:150849600-150851200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:150849600-150851600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:150849600-150853400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:150849600-150853600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:150849800-150850200	Flanking Active TSS	Dnd41	blood
14	chr1:150849800-150850200	Flanking Active TSS	HepG2	liver
15	chr1:150849800-150850200	Flanking Active TSS	K562	blood
16	chr1:150849800-150850200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:150849800-150851400	Weak transcription	Thymus	Thymus
18	chr1:150849800-150853000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:150849800-150853000	Weak transcription	Fetal Lung	lung
20	chr1:150849800-150853400	Weak transcription	HSMM	muscle
21	chr1:150849800-150853600	Weak transcription	HSMMtube	muscle
22	chr1:150849800-150853600	Weak transcription	NH-A	brain
23	chr1:150849800-150854200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:150850000-150850200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:150850000-150850200	Enhancers	Primary B cells from cord blood	blood
26	chr1:150850000-150850200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr1:150850000-150850200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:150850000-150850200	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr1:150850000-150850200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:150850000-150850200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr1:150850000-150850200	Enhancers	Hela-S3	cervix
32	chr1:150850000-150850400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:150850000-150850400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:150850000-150850400	Enhancers	Liver	Liver
35	chr1:150850000-150851200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:150850000-150851400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:150850000-150851400	Weak transcription	Osteobl	bone
38	chr1:150850000-150851600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:150850000-150851600	Weak transcription	NHDF-Ad	bronchial
40	chr1:150850000-150852600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:150850000-150853000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:150850000-150853400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:150850000-150853400	Weak transcription	Adipose Nuclei	Adipose
44	chr1:150850000-150853400	Weak transcription	Placenta	Placenta
45	chr1:150850000-150853400	Weak transcription	HMEC	breast
46	chr1:150850000-150853600	Weak transcription	NHEK	skin
47	chr1:150850000-150855200	Weak transcription	GM12878-XiMat	blood

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