Variant report

Variant	rs9459649
Chromosome Location	chr6:166727745-166727746
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:166726149..166728361-chr6:166730618..166732594,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10946152	0.87[ASN][1000 genomes]
rs10946154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946155	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10946156	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12524268	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12526794	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662924	0.87[ASN][1000 genomes]
rs13218257	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1575145	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710040	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55936781	0.87[ASN][1000 genomes]
rs6913024	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6913025	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935260	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6935275	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9457164	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9459644	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9459648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9459650	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9459651	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv886936	chr6:166714024-166731289	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9459649	CASD1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166722600-166732800	Weak transcription	GM12878-XiMat	blood
2	chr6:166722600-166735600	Weak transcription	Brain Angular Gyrus	brain
3	chr6:166722800-166731200	Weak transcription	Spleen	Spleen
4	chr6:166723000-166731400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:166723000-166732000	Weak transcription	Gastric	stomach
6	chr6:166723200-166732400	Weak transcription	Liver	Liver
7	chr6:166723200-166735400	Weak transcription	Brain Substantia Nigra	brain
8	chr6:166723200-166735600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:166723200-166738800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
11	chr6:166723600-166735800	Weak transcription	Brain Anterior Caudate	brain
12	chr6:166723800-166736000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:166724200-166732400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr6:166725400-166732200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:166726000-166731400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:166726200-166731400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:166726200-166731600	Weak transcription	Thymus	Thymus
18	chr6:166726400-166732600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:166726600-166731400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:166726600-166731800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:166726800-166731800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:166726800-166731800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:166726800-166732000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:166727000-166731200	Enhancers	Fetal Intestine Small	intestine
25	chr6:166727000-166731200	Weak transcription	K562	blood
26	chr6:166727000-166732000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:166727000-166732400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:166727200-166728000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:166727200-166728200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:166727200-166731800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:166727200-166732000	Weak transcription	Fetal Brain Female	brain
32	chr6:166727200-166732600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:166727400-166728000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:166727400-166728200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:166727400-166728600	Weak transcription	Fetal Intestine Large	intestine
36	chr6:166727400-166729200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:166727400-166732200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:166727400-166732200	Weak transcription	Fetal Thymus	thymus
39	chr6:166727400-166732400	Weak transcription	Dnd41	blood
40	chr6:166727400-166734600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:166727400-166734800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:166727400-166736400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:166727400-166739000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:166727600-166727800	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr6:166727600-166736400	Weak transcription	Placenta Amnion	Placenta Amnion

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