Variant report

Variant	rs6502560
Chromosome Location	chr17:16984346-16984347
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16945076..16946861-chr17:16983855..16986072,2	MCF-7	breast:
2	chr17:16983913..16986213-chr17:16997467..16999480,2	MCF-7	breast:
3	chr17:16984318..16990325-chr17:16990439..16995530,6	K562	blood:
4	chr17:16956631..16959260-chr17:16983096..16985186,2	MCF-7	breast:
5	chr17:16978722..16982652-chr17:16983061..16985478,3	K562	blood:
6	chr17:16784922..16787392-chr17:16982105..16984669,2	K562	blood:

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction
ENSG00000225442	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11867273	1.00[EUR][1000 genomes]
rs11867522	1.00[CEU][hapmap]
rs11867723	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11868052	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11868102	1.00[EUR][1000 genomes]
rs11868191	1.00[EUR][1000 genomes]
rs11868392	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11868908	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11869283	1.00[CEU][hapmap]
rs11869415	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11869423	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11870335	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11870441	1.00[EUR][1000 genomes]
rs11870488	1.00[EUR][1000 genomes]
rs11871120	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs57958042	1.00[EUR][1000 genomes]
rs61729732	1.00[EUR][1000 genomes]
rs6502556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6502557	1.00[YRI][hapmap]
rs6502558	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6502559	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7207396	1.00[EUR][1000 genomes]
rs7209447	1.00[EUR][1000 genomes]
rs7211205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7213477	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7215338	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7215588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7216705	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7220492	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7221151	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7223773	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7225532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7225977	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs8064296	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8065260	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8066280	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8067672	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8067959	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8068587	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8070944	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8073346	1.00[CEU][hapmap]
rs8078661	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8080972	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9890700	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
2	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr17:16973200-16985000	Genic enhancers	A549	lung
4	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:16974000-16995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:16974200-16985200	Enhancers	Brain Angular Gyrus	brain
7	chr17:16974400-16985200	Genic enhancers	Fetal Intestine Small	intestine
8	chr17:16975800-16984600	Strong transcription	Primary B cells from cord blood	blood
9	chr17:16977200-16991200	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:16977400-16992400	Strong transcription	Hela-S3	cervix
11	chr17:16978600-16984600	Genic enhancers	Gastric	stomach
12	chr17:16978600-16991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:16978800-16986400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr17:16978800-16996800	Strong transcription	Dnd41	blood
15	chr17:16979000-16984800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr17:16979000-16988600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:16979000-16989000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr17:16979200-16991400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr17:16979400-16990000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr17:16979400-16991200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr17:16979400-16991400	Strong transcription	Primary T cells from cord blood	blood
22	chr17:16979600-16985000	Genic enhancers	Rectal Mucosa Donor 29	rectum
23	chr17:16979600-16985000	Genic enhancers	Stomach Smooth Muscle	stomach
24	chr17:16979600-16986000	Weak transcription	HUVEC	blood vessel
25	chr17:16979600-16989000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr17:16979600-16989400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr17:16979800-16984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr17:16979800-16992200	Strong transcription	Thymus	Thymus
29	chr17:16980200-16985000	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr17:16980600-16984400	Strong transcription	Primary hematopoietic stem cells	blood
31	chr17:16980600-16985000	Enhancers	Fetal Heart	heart
32	chr17:16980800-16984600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:16981000-16986200	Enhancers	Stomach Mucosa	stomach
34	chr17:16981200-16984400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:16981200-16984800	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr17:16981200-16985000	Genic enhancers	Placenta	Placenta
37	chr17:16981200-16985200	Enhancers	Right Atrium	heart
38	chr17:16981200-16985200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
39	chr17:16981600-16984400	Enhancers	Liver	Liver
40	chr17:16981600-16985000	Enhancers	Colonic Mucosa	Colon
41	chr17:16981600-16991600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:16981600-16995000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:16981600-16995400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr17:16981800-16984600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr17:16981800-16985000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:16981800-16985200	Enhancers	Brain Cingulate Gyrus	brain
47	chr17:16981800-16985200	Enhancers	Left Ventricle	heart
48	chr17:16981800-16987600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:16981800-16990200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:16981800-16990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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