Variant report

Variant	rs16949270
Chromosome Location	chr17:45982473-45982474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45981397..45984686-chr17:45985250..45989369,5	K562	blood:
2	chr17:45980692..45982810-chr17:45985460..45986987,2	MCF-7	breast:
3	chr17:45920976..45922650-chr17:45981473..45983982,2	MCF-7	breast:
4	chr17:45981911..45983503-chr17:45998627..46000923,2	K562	blood:
5	chr17:45981534..45985192-chr17:45991810..45993717,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1133221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12232488	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12453773	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16949296	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];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs16949651	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs16951519	0.88[GIH][hapmap]
rs17616799	0.84[ASW][hapmap];0.93[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.94[MKK][hapmap];0.91[AFR][1000 genomes]
rs1986694	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2240119	0.94[GIH][hapmap]
rs2240120	0.88[GIH][hapmap]
rs2240121	0.88[GIH][hapmap]
rs2285860	0.94[GIH][hapmap]
rs2325750	0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2525105	0.86[CHB][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs3764393	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4450442	1.00[CEU][hapmap];0.81[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4614773	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55956628	0.91[ASN][1000 genomes]
rs56006220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56124407	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56218899	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56402159	0.94[AFR][1000 genomes]
rs57782323	0.91[AFR][1000 genomes]
rs58695897	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61396871	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61702159	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7213084	0.84[AMR][1000 genomes]
rs7214154	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7217147	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73323310	0.91[ASN][1000 genomes]
rs757353	0.94[GIH][hapmap]
rs8082055	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9944405	0.82[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.95[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45974200-45982800	Weak transcription	Spleen	Spleen
2	chr17:45974600-45992000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:45975000-45982800	Weak transcription	Gastric	stomach
4	chr17:45975000-45993400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:45975200-45999400	Weak transcription	Fetal Kidney	kidney
6	chr17:45975200-46000400	Weak transcription	Small Intestine	intestine
7	chr17:45975400-45983000	Weak transcription	HUVEC	blood vessel
8	chr17:45975600-45992800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
10	chr17:45976400-45983000	Weak transcription	Aorta	Aorta
11	chr17:45976400-45993200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr17:45976400-45995400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:45976800-45983000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr17:45976800-45987000	Strong transcription	Fetal Intestine Small	intestine
15	chr17:45977000-45984000	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr17:45977200-45984800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:45977600-45982600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr17:45977600-45982800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr17:45977600-45992800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr17:45977600-45995000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr17:45977800-45992000	Weak transcription	Dnd41	blood
22	chr17:45977800-45992600	Weak transcription	Fetal Intestine Large	intestine
23	chr17:45977800-45992600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr17:45977800-45992800	Weak transcription	GM12878-XiMat	blood
25	chr17:45978000-45982800	Weak transcription	Fetal Brain Female	brain
26	chr17:45978400-45985000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr17:45978800-45985200	Enhancers	Psoas Muscle	Psoas
28	chr17:45979200-45987400	Weak transcription	Thymus	Thymus
29	chr17:45979400-45983800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr17:45979400-45984600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr17:45979600-45982600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr17:45979600-45982600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr17:45979600-45983200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr17:45979600-45984600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:45979800-46000400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr17:45980000-45992600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr17:45980000-45992800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr17:45980000-45992800	Weak transcription	Brain Germinal Matrix	brain
39	chr17:45980200-45982600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr17:45980200-45982600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr17:45980200-45986000	Enhancers	Fetal Muscle Trunk	muscle
42	chr17:45980200-46001800	Weak transcription	K562	blood
43	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr17:45980400-45992400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr17:45980400-45993600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr17:45980800-45983000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:45980800-45987000	Enhancers	Left Ventricle	heart
49	chr17:45980800-45992600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr17:45981200-45984000	Genic enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links