Variant report

Variant	rs808589
Chromosome Location	chr6:4873365-4873366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4872004..4874081-chr6:4883324..4885976,2	MCF-7	breast:
2	chr6:4866751..4869142-chr6:4872380..4874648,2	K562	blood:
3	chr6:4865996..4868251-chr6:4873148..4875178,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1265336	0.87[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap]
rs1771884	0.92[ASN][1000 genomes]
rs1883327	0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs233477	0.87[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap]
rs233479	0.91[CHD][hapmap];1.00[JPT][hapmap]
rs55653939	0.86[ASN][1000 genomes]
rs6925763	0.89[ASN][1000 genomes]
rs73364556	0.87[ASN][1000 genomes]
rs808603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs808611	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs808615	0.81[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];0.92[ASN][1000 genomes]
rs808622	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9405783	0.82[AMR][1000 genomes];0.87[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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1015888	chr6:4787784-4883663	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs808589	CDYL	cis	lymphoblastoid	seeQTL
rs808589	C6orf195	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4855200-4882200	Weak transcription	Fetal Stomach	stomach
2	chr6:4856800-4883600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:4858800-4880400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:4859000-4876600	Weak transcription	Ovary	ovary
5	chr6:4865600-4875000	Weak transcription	Aorta	Aorta
6	chr6:4865600-4892200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:4866600-4880200	Weak transcription	HSMM	muscle
8	chr6:4868600-4880200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:4869600-4890000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr6:4870800-4874200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:4871000-4876600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:4871400-4873400	Enhancers	A549	lung
13	chr6:4871400-4875400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:4871400-4891400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:4871400-4892000	Weak transcription	NHEK	skin
16	chr6:4871600-4875800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:4871800-4876400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:4872000-4875200	Enhancers	Brain Substantia Nigra	brain
19	chr6:4872000-4883800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:4872000-4892000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:4872200-4873600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:4872200-4874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:4872200-4874800	Enhancers	Brain Angular Gyrus	brain
24	chr6:4872200-4898800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:4872400-4873600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:4872400-4874400	Weak transcription	K562	blood
27	chr6:4872400-4874800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:4872400-4874800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:4872400-4875400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:4872400-4877000	Weak transcription	Psoas Muscle	Psoas
31	chr6:4872400-4879200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:4872400-4880200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr6:4872400-4880600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr6:4872600-4873600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:4872600-4873800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr6:4872600-4873800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:4872600-4874000	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:4872600-4874000	Weak transcription	HMEC	breast
39	chr6:4872600-4874600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr6:4872600-4877000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:4872800-4874000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:4872800-4874000	Weak transcription	Lung	lung
43	chr6:4872800-4874000	Weak transcription	Right Atrium	heart
44	chr6:4872800-4874600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:4872800-4874800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:4872800-4875000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:4872800-4877000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:4873000-4873800	Enhancers	HUVEC	blood vessel
49	chr6:4873000-4874000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:4873000-4874000	Weak transcription	Left Ventricle	heart

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