Variant report

Variant	rs12004732
Chromosome Location	chr9:26942447-26942448
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:26938009..26940590-chr9:26940591..26942601,2	K562	blood:
2	chr9:26941085..26943170-chr9:26955026..26957108,2	K562	blood:
3	chr9:26941187..26942986-chr9:26945124..26947571,3	K562	blood:
4	chr9:26898930..26900769-chr9:26941051..26942769,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137055	Chromatin interaction
ENSG00000234676	Chromatin interaction
ENSG00000096872	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10511793	0.93[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10738762	0.85[TSI][hapmap]
rs10757635	0.85[TSI][hapmap]
rs10812492	0.80[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10812500	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10967594	0.80[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12002260	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12342005	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16910888	0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16910895	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59274950	0.85[ASN][1000 genomes]
rs62544439	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62544443	0.97[ASN][1000 genomes]
rs62544444	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62544450	0.97[ASN][1000 genomes]
rs62544451	0.97[ASN][1000 genomes]
rs62544452	0.97[ASN][1000 genomes]
rs6475945	0.83[CEU][hapmap]
rs6475947	0.83[CEU][hapmap]
rs6475948	0.87[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7019692	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7023230	0.97[ASN][1000 genomes]
rs7024415	0.84[EUR][1000 genomes]
rs7032756	0.81[TSI][hapmap]
rs7035755	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7038218	0.88[CEU][hapmap]
rs7039400	0.90[GIH][hapmap]
rs7040516	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7042447	0.83[CEU][hapmap]
rs7045881	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7851339	0.97[ASN][1000 genomes]
rs7851423	0.88[ASN][1000 genomes]
rs7856462	0.83[CEU][hapmap]
rs7860542	0.85[CEU][hapmap]
rs7866718	0.85[ASN][1000 genomes]
rs7868158	0.83[CEU][hapmap]
rs7871097	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7871286	0.80[ASW][hapmap];0.94[CEU][hapmap];0.96[GIH][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]

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	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12004732	C9orf82	cis	cerebellum	SCAN
rs12004732	IFT74	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26916800-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:26925800-26945200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:26926000-26945200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:26926000-26945200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:26926000-26945400	Weak transcription	HSMMtube	muscle
6	chr9:26926600-26944200	Weak transcription	NHEK	skin
7	chr9:26926600-26945600	Weak transcription	Fetal Kidney	kidney
8	chr9:26927400-26943800	Weak transcription	Pancreas	Pancrea
9	chr9:26927400-26945600	Weak transcription	Fetal Thymus	thymus
10	chr9:26927800-26945600	Weak transcription	Colonic Mucosa	Colon
11	chr9:26928400-26945200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:26928400-26945400	Weak transcription	NH-A	brain
13	chr9:26928600-26943600	Weak transcription	NHLF	lung
14	chr9:26928600-26945000	Weak transcription	Osteobl	bone
15	chr9:26928600-26945600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:26928800-26943800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:26928800-26944400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:26928800-26944600	Weak transcription	HMEC	breast
19	chr9:26932400-26945400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:26935200-26943000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:26935200-26945400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr9:26936400-26945400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:26936600-26944200	Weak transcription	Liver	Liver
24	chr9:26936800-26943200	Weak transcription	Ovary	ovary
25	chr9:26936800-26943200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:26936800-26944000	Weak transcription	Brain Angular Gyrus	brain
27	chr9:26936800-26944600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:26936800-26945200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:26936800-26945200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:26936800-26945400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr9:26936800-26945600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:26936800-26945600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:26936800-26945600	Weak transcription	Aorta	Aorta
34	chr9:26937200-26945200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr9:26938000-26944000	Weak transcription	Colon Smooth Muscle	Colon
36	chr9:26938200-26944600	Weak transcription	Brain Anterior Caudate	brain
37	chr9:26938400-26942600	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr9:26938400-26944000	Weak transcription	HSMM	muscle
39	chr9:26938400-26945200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:26938400-26945200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:26938400-26945400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:26938400-26945400	Weak transcription	Fetal Lung	lung
43	chr9:26938400-26945600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:26938600-26943200	Weak transcription	Primary B cells from cord blood	blood
45	chr9:26938600-26943200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:26938600-26943200	Weak transcription	Psoas Muscle	Psoas
47	chr9:26938600-26943600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:26938600-26943800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:26938600-26945400	Weak transcription	Fetal Intestine Small	intestine
50	chr9:26938600-26945600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links