Variant report

Variant	rs2954779
Chromosome Location	chr17:15361941-15361942
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15353703..15358541-chr17:15361568..15365038,4	K562	blood:
2	chr17:15353769..15358146-chr17:15361916..15367322,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239704	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1019092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10432020	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1548679	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1548680	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17842195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2108757	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2190914	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2323734	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2875140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2906973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2906977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2906978	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs2906979	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2906980	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2906981	0.84[ASN][1000 genomes]
rs2906982	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2906983	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906984	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2906985	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2954759	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs2954760	0.88[GIH][hapmap]
rs2954761	0.85[JPT][hapmap]
rs2954762	0.88[GIH][hapmap]
rs2954767	0.81[AMR][1000 genomes]
rs2954768	0.89[AMR][1000 genomes]
rs2954770	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2954771	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2954772	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2954773	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2954774	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2954775	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2954776	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2954777	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2954778	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56055931	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6502450	0.81[AMR][1000 genomes]
rs728854	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729355	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs729356	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729357	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887033	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887034	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15338400-15362200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr17:15339600-15367000	Weak transcription	A549	lung
3	chr17:15340600-15366200	Weak transcription	Gastric	stomach
4	chr17:15340600-15366800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr17:15340600-15399600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:15341400-15366800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:15341400-15366800	Weak transcription	Esophagus	oesophagus
8	chr17:15341400-15368400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:15341400-15375800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr17:15348600-15366800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr17:15349400-15368800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr17:15354800-15362400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr17:15356200-15366000	Weak transcription	Hela-S3	cervix
14	chr17:15356800-15378000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:15357800-15366400	Weak transcription	Brain Germinal Matrix	brain
16	chr17:15357800-15375800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:15359200-15362000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr17:15359200-15404600	Weak transcription	Primary T cells from cord blood	blood
19	chr17:15359400-15363600	Enhancers	Fetal Muscle Leg	muscle
20	chr17:15359400-15386600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:15359600-15362200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr17:15359600-15363200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr17:15359600-15383000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr17:15359800-15362000	Enhancers	Fetal Heart	heart
25	chr17:15359800-15362000	Enhancers	Psoas Muscle	Psoas
26	chr17:15359800-15362200	Enhancers	Brain Cingulate Gyrus	brain
27	chr17:15359800-15362200	Enhancers	Fetal Lung	lung
28	chr17:15359800-15362200	Enhancers	Left Ventricle	heart
29	chr17:15359800-15362200	Enhancers	Right Atrium	heart
30	chr17:15359800-15362800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr17:15360000-15362200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr17:15360200-15362000	Enhancers	Fetal Brain Female	brain
33	chr17:15360200-15362200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:15360200-15369600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:15360600-15362200	Enhancers	Fetal Brain Male	brain
36	chr17:15360800-15362200	Enhancers	Brain Substantia Nigra	brain
37	chr17:15360800-15362600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr17:15360800-15364000	Enhancers	Fetal Muscle Trunk	muscle
39	chr17:15360800-15367000	Weak transcription	Spleen	Spleen
40	chr17:15361000-15362000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr17:15361000-15362000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:15361000-15362000	Enhancers	Fetal Stomach	stomach
43	chr17:15361000-15362000	Enhancers	NHLF	lung
44	chr17:15361000-15362200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr17:15361000-15362400	Enhancers	Brain Angular Gyrus	brain
46	chr17:15361000-15362400	Enhancers	Brain Anterior Caudate	brain
47	chr17:15361000-15362600	Enhancers	Adipose Nuclei	Adipose
48	chr17:15361000-15366400	Weak transcription	Fetal Intestine Large	intestine
49	chr17:15361200-15362000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:15361200-15362000	Enhancers	Colon Smooth Muscle	Colon

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