Variant report

Variant	rs16949296
Chromosome Location	chr17:45984949-45984950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45981534..45985192-chr17:45991810..45993717,3	MCF-7	breast:
2	chr17:45982730..45985492-chr17:46018085..46020258,2	MCF-7	breast:
3	chr17:45922908..45925647-chr17:45983799..45986055,2	MCF-7	breast:
4	chr17:45983643..45985330-chr17:45987212..45990187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234494	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1133221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12232488	0.94[EUR][1000 genomes]
rs12453773	0.92[EUR][1000 genomes]
rs16949270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16949427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16949651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17616799	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs1986694	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2325750	0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2525105	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs3764393	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450442	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs4614773	0.92[EUR][1000 genomes]
rs55956628	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs56006220	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56124407	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56218899	0.91[EUR][1000 genomes]
rs58695897	0.92[EUR][1000 genomes]
rs61702159	0.92[EUR][1000 genomes]
rs7214154	0.92[EUR][1000 genomes]
rs7217147	0.92[EUR][1000 genomes]
rs73323310	0.97[ASN][1000 genomes]
rs8082055	0.92[EUR][1000 genomes]
rs9944405	0.81[CHB][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45974600-45992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
4	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
5	chr17:45975600-45992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
7	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:45976800-45987000	Strong transcription	Fetal Intestine Small	intestine
10	chr17:45977600-45992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr17:45977800-45992000	Weak transcription	Dnd41	blood
13	chr17:45977800-45992600	Weak transcription	Fetal Intestine Large	intestine
14	chr17:45977800-45992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr17:45977800-45992800	Weak transcription	GM12878-XiMat	blood
16	chr17:45978400-45985000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:45978800-45985200	Enhancers	Psoas Muscle	Psoas
18	chr17:45979200-45987400	Weak transcription	Thymus	Thymus
19	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr17:45980000-45992600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr17:45980000-45992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr17:45980000-45992800	Weak transcription	Brain Germinal Matrix	brain
23	chr17:45980200-45986000	Enhancers	Fetal Muscle Trunk	muscle
24	chr17:45980200-46001800	Weak transcription	K562	blood
25	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr17:45980400-45992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr17:45980800-45987000	Enhancers	Left Ventricle	heart
30	chr17:45980800-45992600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:45981400-45985000	Enhancers	Right Atrium	heart
32	chr17:45981600-45985200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:45981600-45985200	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr17:45981600-45985400	Enhancers	Brain Hippocampus Middle	brain
35	chr17:45981600-45985600	Enhancers	Lung	lung
36	chr17:45981600-45986000	Enhancers	Fetal Heart	heart
37	chr17:45981800-45985200	Enhancers	Brain Cingulate Gyrus	brain
38	chr17:45981800-45985400	Enhancers	Right Ventricle	heart
39	chr17:45981800-45987200	Enhancers	Adipose Nuclei	Adipose
40	chr17:45982200-45985200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:45982200-45988400	Strong transcription	Primary T cells from cord blood	blood
42	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
43	chr17:45982600-45985800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr17:45982600-45992600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:45982600-45992600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr17:45982600-45992800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr17:45982600-45996200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:45982800-45985800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr17:45982800-45993000	Weak transcription	NHEK	skin
50	chr17:45983000-45985000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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