Variant report

Variant	rs228870
Chromosome Location	chr17:64487670-64487671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:64480731..64483627-chr17:64487190..64489494,2	MCF-7	breast:
2	chr17:64429428..64432036-chr17:64486518..64489080,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1473933	0.95[ASN][1000 genomes]
rs1473934	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1514653	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1877846	0.95[ASN][1000 genomes]
rs1877847	0.95[ASN][1000 genomes]
rs1877848	0.94[ASN][1000 genomes]
rs1980118	0.82[ASN][1000 genomes]
rs228874	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs228877	0.95[ASN][1000 genomes]
rs228878	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs228879	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs228881	0.87[EUR][1000 genomes]
rs228884	0.84[EUR][1000 genomes]
rs228887	0.84[EUR][1000 genomes]
rs228888	0.84[EUR][1000 genomes]
rs2361484	0.95[ASN][1000 genomes]
rs2361485	0.95[ASN][1000 genomes]
rs2535659	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2885290	0.95[ASN][1000 genomes]
rs4270211	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4375700	0.95[ASN][1000 genomes]
rs4622543	0.95[ASN][1000 genomes]
rs4791053	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4791054	0.95[ASN][1000 genomes]
rs4791055	0.95[ASN][1000 genomes]
rs4791060	0.82[EUR][1000 genomes]
rs57078491	0.89[AFR][1000 genomes]
rs62070456	0.86[AFR][1000 genomes]
rs6504439	0.95[ASN][1000 genomes]
rs6504440	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7211424	0.95[ASN][1000 genomes]
rs7218008	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7218053	0.95[ASN][1000 genomes]
rs7218480	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7221053	0.83[ASN][1000 genomes]
rs7225362	0.89[ASN][1000 genomes]
rs8064886	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8068988	0.92[ASN][1000 genomes]
rs8068989	0.94[ASN][1000 genomes]
rs8069282	0.88[ASN][1000 genomes]
rs8070470	0.95[ASN][1000 genomes]
rs8079527	0.83[ASN][1000 genomes]
rs9896483	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9896922	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9896956	0.95[ASN][1000 genomes]
rs9897124	0.94[ASN][1000 genomes]
rs9897534	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9898205	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9913336	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9915432	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:64465400-64489000	Weak transcription	Gastric	stomach
2	chr17:64465400-64492400	Weak transcription	Aorta	Aorta
3	chr17:64469600-64488800	Weak transcription	Spleen	Spleen
4	chr17:64472000-64487800	Weak transcription	NHLF	lung
5	chr17:64473200-64488800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:64479000-64499000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr17:64481600-64488800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr17:64481800-64487800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr17:64481800-64488600	Weak transcription	NH-A	brain
10	chr17:64481800-64489600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr17:64482000-64488600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:64482000-64488800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr17:64482000-64488800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr17:64482000-64488800	Weak transcription	Fetal Brain Female	brain
15	chr17:64482200-64488200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:64482400-64488000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:64483800-64492800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:64484800-64489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:64485000-64491000	Enhancers	HepG2	liver
20	chr17:64485000-64499200	Weak transcription	Fetal Kidney	kidney
21	chr17:64485600-64490600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr17:64485600-64490800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr17:64485800-64488800	Weak transcription	Fetal Intestine Small	intestine
24	chr17:64485800-64490800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr17:64485800-64498800	Weak transcription	Fetal Intestine Large	intestine
26	chr17:64486800-64488200	Weak transcription	HSMM	muscle
27	chr17:64486800-64491000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr17:64487000-64487800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:64487000-64489000	Enhancers	NHDF-Ad	bronchial
30	chr17:64487000-64489400	Enhancers	Fetal Thymus	thymus
31	chr17:64487000-64490600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr17:64487000-64490800	Enhancers	Brain Substantia Nigra	brain
33	chr17:64487000-64491000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr17:64487000-64491200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:64487000-64491600	Enhancers	K562	blood
36	chr17:64487200-64487800	Enhancers	Primary T cells from cord blood	blood
37	chr17:64487200-64488400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr17:64487200-64488800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:64487200-64488800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:64487200-64490600	Enhancers	Brain Hippocampus Middle	brain
41	chr17:64487200-64490800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr17:64487400-64487800	Enhancers	Small Intestine	intestine
43	chr17:64487400-64488800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr17:64487400-64488800	Enhancers	A549	lung
45	chr17:64487400-64489200	Enhancers	Liver	Liver
46	chr17:64487400-64489400	Enhancers	Osteobl	bone
47	chr17:64487400-64489600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:64487400-64490600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr17:64487400-64490600	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr17:64487400-64490800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links