Variant report

Variant	rs2067986
Chromosome Location	chr9:101816399-101816400
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	chr9:101815426..101817191-chr9:101905966..101908398,2	K562	blood:

Variant related genes	Relation type
ENSG00000252942	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10512262	1.00[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs12001981	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352174	0.93[CEU][hapmap];0.83[ASN][1000 genomes]
rs13291453	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13296166	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13302368	1.00[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs1360686	1.00[LWK][hapmap]
rs1537505	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1537506	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918146	0.81[ASN][1000 genomes]
rs16918148	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs16918154	0.84[ASN][1000 genomes]
rs16918163	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34382379	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34654420	0.84[ASN][1000 genomes]
rs34749011	0.82[ASN][1000 genomes]
rs35413276	0.82[ASN][1000 genomes]
rs3739799	1.00[ASW][hapmap]
rs4563947	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4631520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478969	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7019613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7034847	1.00[ASW][hapmap]
rs7036916	0.93[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs7851079	0.93[CEU][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap]
rs7854112	0.93[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs7857774	0.93[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs928522	1.00[CEU][hapmap]

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	nsv466442	chr9:101788522-101816399	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv614954	chr9:101788522-101816399	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2067986	C9orf30	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101782000-101819800	Weak transcription	Colonic Mucosa	Colon
2	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
3	chr9:101798400-101819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr9:101804000-101820000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:101805800-101819400	Strong transcription	Adipose Nuclei	Adipose
6	chr9:101805800-101820600	Weak transcription	Right Ventricle	heart
7	chr9:101806600-101817000	Weak transcription	Left Ventricle	heart
8	chr9:101807000-101831800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr9:101807400-101819000	Strong transcription	Fetal Stomach	stomach
10	chr9:101807600-101831800	Strong transcription	Fetal Muscle Leg	muscle
11	chr9:101807800-101819800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:101808400-101817200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:101809200-101821600	Weak transcription	Brain Anterior Caudate	brain
14	chr9:101810600-101817600	Weak transcription	Ovary	ovary
15	chr9:101810600-101819800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr9:101811200-101820000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:101811400-101816400	Enhancers	K562	blood
18	chr9:101812200-101818600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:101813000-101817600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:101813000-101819400	Weak transcription	NHLF	lung
21	chr9:101813200-101833000	Weak transcription	Lung	lung
22	chr9:101813400-101817400	Weak transcription	NHEK	skin
23	chr9:101813600-101817000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:101813600-101825600	Weak transcription	Aorta	Aorta
25	chr9:101814000-101819200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:101814200-101817000	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr9:101814200-101819200	Weak transcription	NHDF-Ad	bronchial
28	chr9:101814200-101819400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr9:101814200-101820200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:101814200-101826600	Weak transcription	Fetal Intestine Large	intestine
31	chr9:101814200-101829400	Weak transcription	Fetal Intestine Small	intestine
32	chr9:101814400-101816600	Genic enhancers	Placenta	Placenta
33	chr9:101814400-101819000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr9:101814400-101820200	Enhancers	Thymus	Thymus
35	chr9:101814600-101816400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr9:101814600-101816400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:101814600-101816400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:101814600-101816600	Enhancers	Duodenum Mucosa	Duodenum
39	chr9:101814600-101816600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:101814600-101819600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr9:101814800-101816400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:101814800-101816400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:101814800-101816600	Enhancers	Primary B cells from peripheral blood	blood
44	chr9:101814800-101816600	Enhancers	Primary hematopoietic stem cells	blood
45	chr9:101814800-101816600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:101814800-101816600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:101814800-101816800	Weak transcription	Osteobl	bone
48	chr9:101814800-101817000	Enhancers	Fetal Thymus	thymus
49	chr9:101814800-101817400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:101814800-101819200	Enhancers	Primary T cells from cord blood	blood

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