Variant report

Variant	rs2954760
Chromosome Location	chr17:15342097-15342098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15336028..15339604-chr17:15340732..15344968,3	MCF-7	breast:
2	chr17:15340965..15343632-chr17:15346511..15350104,3	K562	blood:

Variant related genes	Relation type
ENSG00000234324	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1986881	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2108757	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs2875140	0.88[GIH][hapmap];0.80[MEX][hapmap]
rs2906985	0.90[GIH][hapmap];0.80[MEX][hapmap]
rs2906987	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906989	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906990	0.97[EUR][1000 genomes]
rs2954749	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954750	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954752	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954753	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954754	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954755	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954756	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954759	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954761	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954763	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954764	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954767	0.90[JPT][hapmap]
rs2954768	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2954778	0.90[GIH][hapmap];0.85[MEX][hapmap]
rs2954779	0.88[GIH][hapmap]
rs6502450	0.90[JPT][hapmap]
rs728854	0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic 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	14 gene(s)	inside rSNPs	diseases
6	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15333600-15361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:15335400-15343000	Enhancers	Fetal Intestine Large	intestine
3	chr17:15335600-15348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:15336600-15345200	Enhancers	Fetal Heart	heart
5	chr17:15336600-15347600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:15338400-15342400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:15338400-15362200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:15339400-15354800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:15339400-15358800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr17:15339600-15367000	Weak transcription	A549	lung
11	chr17:15340000-15355400	Weak transcription	Hela-S3	cervix
12	chr17:15340000-15355800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:15340000-15357400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr17:15340200-15344200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr17:15340200-15345000	Weak transcription	HSMMtube	muscle
16	chr17:15340200-15345200	Weak transcription	Brain Angular Gyrus	brain
17	chr17:15340200-15345600	Weak transcription	Fetal Brain Male	brain
18	chr17:15340200-15348000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr17:15340200-15354800	Weak transcription	Osteobl	bone
20	chr17:15340200-15355600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:15340400-15342200	Weak transcription	HMEC	breast
22	chr17:15340400-15342800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr17:15340400-15342800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr17:15340400-15343000	Genic enhancers	Fetal Intestine Small	intestine
25	chr17:15340400-15343200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr17:15340400-15343800	Weak transcription	Placenta	Placenta
27	chr17:15340400-15345000	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr17:15340400-15345000	Weak transcription	Brain Anterior Caudate	brain
29	chr17:15340400-15345800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:15340400-15345800	Weak transcription	NHDF-Ad	bronchial
31	chr17:15340400-15348000	Weak transcription	Ovary	ovary
32	chr17:15340400-15355600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr17:15340400-15356000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr17:15340400-15359000	Weak transcription	Colon Smooth Muscle	Colon
35	chr17:15340600-15342600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr17:15340600-15343000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr17:15340600-15343600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr17:15340600-15343800	Weak transcription	Right Ventricle	heart
39	chr17:15340600-15344800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr17:15340600-15345000	Weak transcription	Brain Substantia Nigra	brain
41	chr17:15340600-15345200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr17:15340600-15345200	Weak transcription	Brain Hippocampus Middle	brain
43	chr17:15340600-15348000	Weak transcription	Primary T cells from cord blood	blood
44	chr17:15340600-15348000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:15340600-15359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr17:15340600-15360200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr17:15340600-15360200	Weak transcription	Fetal Thymus	thymus
48	chr17:15340600-15366200	Weak transcription	Gastric	stomach
49	chr17:15340600-15366800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links