Variant report

Variant	rs228878
Chromosome Location	chr17:64505780-64505781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:64498031..64500928-chr17:64503765..64506481,3	MCF-7	breast:
2	chr17:64299701..64302509-chr17:64504832..64506690,3	MCF-7	breast:
3	chr17:64499401..64501930-chr17:64504222..64508278,5	MCF-7	breast:
4	chr17:64503426..64505908-chr17:64565929..64568262,2	MCF-7	breast:
5	chr17:64343831..64346632-chr17:64504391..64506727,2	MCF-7	breast:
6	chr17:64503626..64507528-chr17:64509993..64514174,5	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1473933	1.00[ASN][1000 genomes]
rs1473934	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514653	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877846	1.00[ASN][1000 genomes]
rs1877847	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1877848	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs1980118	0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2056071	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs228870	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs228874	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs228877	1.00[ASN][1000 genomes]
rs228879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs228881	0.87[EUR][1000 genomes]
rs228884	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs228887	0.84[EUR][1000 genomes]
rs228888	0.84[EUR][1000 genomes]
rs2361484	1.00[ASN][1000 genomes]
rs2361485	1.00[ASN][1000 genomes]
rs2535659	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885290	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4270211	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4375700	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4622543	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4791053	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4791055	0.98[ASN][1000 genomes]
rs4791060	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs57078491	0.83[AFR][1000 genomes]
rs62070456	0.81[AFR][1000 genomes]
rs6504439	1.00[ASN][1000 genomes]
rs6504440	0.90[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7211424	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7218008	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7218053	1.00[ASN][1000 genomes]
rs7218480	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7221053	0.87[ASN][1000 genomes]
rs7225362	0.94[ASN][1000 genomes]
rs8064886	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068988	0.96[ASN][1000 genomes]
rs8068989	0.98[ASN][1000 genomes]
rs8069282	0.92[ASN][1000 genomes]
rs8070470	1.00[ASN][1000 genomes]
rs8079527	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9896483	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896922	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9896956	1.00[ASN][1000 genomes]
rs9897124	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9897534	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9898205	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9913336	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9915432	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057876	chr17:64401469-64802341	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv543407	chr17:64401469-64802341	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv457883	chr17:64410915-64510410	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv575897	chr17:64410915-64510410	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457887	chr17:64410915-64518507	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv575898	chr17:64410915-64518507	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv817351	chr17:64420296-64742555	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv948353	chr17:64454960-64619767	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv948335	chr17:64454960-64745690	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1056765	chr17:64486268-64661890	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1058004	chr17:64504644-64592577	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:64490400-64520800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:64490800-64505800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr17:64491000-64517800	Weak transcription	Dnd41	blood
4	chr17:64496200-64510800	Weak transcription	Primary T cells from cord blood	blood
5	chr17:64499800-64513400	Weak transcription	Brain Germinal Matrix	brain
6	chr17:64502200-64508200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr17:64502400-64507200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr17:64502400-64508200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:64502400-64508400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr17:64502600-64506000	Enhancers	Small Intestine	intestine
11	chr17:64502600-64506600	Flanking Active TSS	A549	lung
12	chr17:64502600-64506600	Enhancers	NHLF	lung
13	chr17:64502600-64507600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr17:64502600-64508400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr17:64502800-64506400	Enhancers	Brain Hippocampus Middle	brain
16	chr17:64502800-64506400	Enhancers	Ovary	ovary
17	chr17:64502800-64506600	Enhancers	NHDF-Ad	bronchial
18	chr17:64502800-64506800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:64502800-64507600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:64502800-64508000	Enhancers	HMEC	breast
21	chr17:64503000-64506000	Enhancers	HepG2	liver
22	chr17:64503000-64506400	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr17:64503000-64506600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:64503000-64506800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:64503000-64507600	Enhancers	HUVEC	blood vessel
26	chr17:64503000-64507800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:64503000-64508200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr17:64503000-64508200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr17:64503200-64506000	Enhancers	Colon Smooth Muscle	Colon
30	chr17:64503200-64506000	Enhancers	Stomach Smooth Muscle	stomach
31	chr17:64503200-64506200	Enhancers	Liver	Liver
32	chr17:64503200-64506800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr17:64503400-64506000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr17:64503400-64506000	Flanking Active TSS	Hela-S3	cervix
35	chr17:64503400-64506200	Enhancers	Brain Cingulate Gyrus	brain
36	chr17:64503400-64506400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr17:64503400-64506600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr17:64503400-64506600	Enhancers	Stomach Mucosa	stomach
39	chr17:64503600-64506200	Enhancers	HSMMtube	muscle
40	chr17:64503600-64506400	Enhancers	Brain Substantia Nigra	brain
41	chr17:64503600-64506600	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr17:64503600-64507800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:64503600-64508200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr17:64503800-64511800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:64504000-64510400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr17:64504200-64505800	Enhancers	Pancreas	Pancrea
47	chr17:64504200-64505800	Enhancers	Right Ventricle	heart
48	chr17:64504200-64506000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr17:64504200-64506200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr17:64504200-64506600	Enhancers	NH-A	brain

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