Variant report

Variant	rs2906989
Chromosome Location	chr17:15338256-15338257
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	chr17:15336028..15339604-chr17:15340732..15344968,3	MCF-7	breast:
2	chr17:15205804..15207784-chr17:15337201..15339636,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1986881	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2108757	0.90[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs2190914	0.82[AMR][1000 genomes]
rs2875140	0.88[GIH][hapmap];0.80[MEX][hapmap]
rs2906979	0.82[AMR][1000 genomes]
rs2906985	0.90[GIH][hapmap];0.80[MEX][hapmap]
rs2906987	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2906990	0.94[EUR][1000 genomes]
rs2954749	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954750	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2954752	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954753	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954754	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954755	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954756	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954761	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[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];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954763	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954764	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2954767	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs2954768	0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2954776	0.82[AMR][1000 genomes]
rs2954777	0.81[AMR][1000 genomes]
rs2954778	0.90[GIH][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs2954779	0.88[GIH][hapmap]
rs6502450	0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs728854	0.81[ASW][hapmap];0.90[GIH][hapmap];0.82[AMR][1000 genomes]
rs729357	0.82[AMR][1000 genomes]
rs887034	0.81[AMR][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:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15326000-15340200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:15326400-15340600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr17:15326600-15340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:15328800-15339600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:15329000-15339400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr17:15329800-15340000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:15331000-15339400	Weak transcription	Esophagus	oesophagus
8	chr17:15332800-15340400	Enhancers	Fetal Muscle Leg	muscle
9	chr17:15333000-15340600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:15333000-15340600	Weak transcription	Aorta	Aorta
11	chr17:15333000-15340600	Weak transcription	Thymus	Thymus
12	chr17:15333200-15339000	Enhancers	Fetal Muscle Trunk	muscle
13	chr17:15333400-15340400	Enhancers	Fetal Stomach	stomach
14	chr17:15333600-15361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:15334200-15339600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:15334600-15339200	Weak transcription	Brain Substantia Nigra	brain
17	chr17:15334600-15339400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:15335000-15339400	Weak transcription	Brain Angular Gyrus	brain
19	chr17:15335000-15339400	Weak transcription	Brain Anterior Caudate	brain
20	chr17:15335000-15339400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr17:15335000-15339600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:15335200-15339600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr17:15335400-15339400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:15335400-15340400	Enhancers	Placenta	Placenta
25	chr17:15335400-15343000	Enhancers	Fetal Intestine Large	intestine
26	chr17:15335600-15340400	Enhancers	Fetal Intestine Small	intestine
27	chr17:15335600-15348000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr17:15335800-15338400	Enhancers	Small Intestine	intestine
29	chr17:15335800-15339800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:15335800-15340600	Enhancers	Fetal Lung	lung
31	chr17:15336000-15338600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr17:15336000-15338600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr17:15336000-15338800	Enhancers	NHLF	lung
34	chr17:15336200-15338400	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr17:15336200-15338400	Enhancers	Placenta Amnion	Placenta Amnion
36	chr17:15336200-15338600	Enhancers	Lung	lung
37	chr17:15336200-15338800	Enhancers	Left Ventricle	heart
38	chr17:15336200-15338800	Enhancers	Right Atrium	heart
39	chr17:15336200-15339000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr17:15336200-15339600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:15336200-15339800	Weak transcription	Brain Germinal Matrix	brain
42	chr17:15336200-15340400	Enhancers	NHDF-Ad	bronchial
43	chr17:15336200-15340800	Enhancers	Adipose Nuclei	Adipose
44	chr17:15336400-15338600	Flanking Active TSS	HepG2	liver
45	chr17:15336400-15339800	Weak transcription	Spleen	Spleen
46	chr17:15336400-15340200	Enhancers	HSMMtube	muscle
47	chr17:15336600-15338800	Enhancers	Colon Smooth Muscle	Colon
48	chr17:15336600-15339800	Weak transcription	Hela-S3	cervix
49	chr17:15336600-15340200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr17:15336600-15341000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links