Variant report

Variant	rs17102252
Chromosome Location	chr1:46989531-46989532
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46913874..46916850-chr1:46987729..46989869,4	K562	blood:
2	chr1:46985914..46991197-chr1:46993744..46997835,5	K562	blood:
3	chr1:46916965..46919039-chr1:46986661..46989583,2	K562	blood:
4	chr1:46985009..46990560-chr1:46990823..46993646,5	K562	blood:
5	chr1:46945138..46947370-chr1:46988064..46989764,2	K562	blood:
6	chr1:46874023..46875964-chr1:46987964..46989966,2	MCF-7	breast:
7	chr1:46986798..46990832-chr1:46991693..46995331,8	K562	blood:
8	chr1:46908155..46911848-chr1:46987375..46989663,3	K562	blood:
9	chr1:46908155..46911848-chr1:46987375..46989961,4	K562	blood:
10	chr1:46975501..46977043-chr1:46987288..46989781,2	K562	blood:
11	chr1:46945870..46948145-chr1:46988064..46989957,2	K562	blood:
12	chr1:46950640..46959255-chr1:46986389..46991936,15	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117480	Chromatin interaction
ENSG00000224863	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11211298	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1258022	1.00[GIH][hapmap]
rs1258028	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1258040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1258042	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1258046	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1320556	1.00[EUR][1000 genomes]
rs13373780	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486164	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2486165	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59291308	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60242607	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60309634	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60791879	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61011128	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61629467	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61691256	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660663	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72894674	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515750	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7518867	0.97[ASN][1000 genomes]
rs7525300	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556404	0.93[ASN][1000 genomes]
rs942253	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv998422	chr1:46969626-47023671	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv534953	chr1:46969626-47023671	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1010578	chr1:46977818-47010579	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46983200-46989800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:46985000-46990200	Enhancers	HMEC	breast
3	chr1:46985800-46989800	Enhancers	Adipose Nuclei	Adipose
4	chr1:46986600-46990000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:46986600-46991200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:46986800-46989600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:46987200-46989800	Flanking Active TSS	K562	blood
8	chr1:46987200-46990600	Enhancers	Esophagus	oesophagus
9	chr1:46987400-46990200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:46987600-46990400	Enhancers	Stomach Mucosa	stomach
11	chr1:46987800-46990000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:46987800-46990000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:46987800-46991000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr1:46987800-46993800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:46988400-46990000	Bivalent Enhancer	Fetal Thymus	thymus
16	chr1:46988400-46992400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:46988400-46992600	Weak transcription	Spleen	Spleen
18	chr1:46988600-46990200	Enhancers	NHEK	skin
19	chr1:46988600-46990400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:46988800-46990200	Enhancers	Hela-S3	cervix
21	chr1:46988800-46991000	Weak transcription	NH-A	brain
22	chr1:46988800-46998600	Weak transcription	Right Ventricle	heart
23	chr1:46989000-46989600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:46989000-46993200	Weak transcription	Pancreas	Pancrea
25	chr1:46989000-46999000	Weak transcription	Gastric	stomach
26	chr1:46989200-46998600	Weak transcription	Right Atrium	heart
27	chr1:46989400-46990800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:46989400-46992600	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links