Variant report

Variant	rs9366007
Chromosome Location	chr6:166732338-166732339
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	chr6:166726149..166728361-chr6:166730618..166732594,2	K562	blood:
2	chr6:166731399..166733245-chr6:166736338..166738185,2	K562	blood:

Variant related genes	Relation type
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10806847	0.95[CEU][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10862	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11168	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2343590	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4470829	0.98[EUR][1000 genomes]
rs4598048	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4709112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4710041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6905635	1.00[CHB][hapmap]
rs6909951	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6918901	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6927168	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs735297	1.00[CHB][hapmap];0.89[CHD][hapmap]
rs7757549	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9355572	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9356476	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9356478	1.00[CEU][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9356479	0.85[AMR][1000 genomes]
rs9366005	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9366006	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9459654	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9366007	SFT2D1	cis	Whole Blood	GTEx
rs9366007	HNRNPA1P49	cis	lung	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

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	chr6:166723200-166732400	Weak transcription	Liver	Liver
4	chr6:166723200-166735400	Weak transcription	Brain Substantia Nigra	brain
5	chr6:166723200-166735600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:166723200-166738800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
8	chr6:166723600-166735800	Weak transcription	Brain Anterior Caudate	brain
9	chr6:166723800-166736000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:166724200-166732400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr6:166726400-166732600	Weak transcription	Primary T cells from cord blood	blood
12	chr6:166727000-166732400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:166727200-166732600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:166727400-166732400	Weak transcription	Dnd41	blood
15	chr6:166727400-166734600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:166727400-166734800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:166727400-166736400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:166727400-166739000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr6:166727600-166736400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:166727800-166733400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:166727800-166736200	Weak transcription	Fetal Lung	lung
22	chr6:166728000-166732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr6:166728000-166732800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:166728000-166733600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:166728000-166735800	Weak transcription	NHLF	lung
26	chr6:166728200-166732600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:166728200-166732600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:166728200-166732800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:166728400-166732400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:166728400-166734800	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:166728400-166736400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:166728600-166732400	Weak transcription	Adipose Nuclei	Adipose
33	chr6:166728600-166735800	Weak transcription	Ovary	ovary
34	chr6:166728600-166736400	Weak transcription	NHDF-Ad	bronchial
35	chr6:166728600-166737800	Weak transcription	Brain Germinal Matrix	brain
36	chr6:166728800-166732400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr6:166728800-166732400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:166729200-166733600	Weak transcription	HepG2	liver
40	chr6:166729200-166734200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:166729200-166744200	Weak transcription	Stomach Mucosa	stomach
42	chr6:166729400-166732400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:166729600-166734200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:166729600-166734800	Weak transcription	Colonic Mucosa	Colon
45	chr6:166729600-166735800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:166729600-166744000	Weak transcription	Small Intestine	intestine
47	chr6:166729800-166733400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:166729800-166733400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:166730000-166734800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:166730000-166734800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links