Variant report

Variant	rs1982151
Chromosome Location	chr9:86617265-86617266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86591997..86594471-chr9:86616779..86619111,2	K562	blood:
2	chr9:86611159..86613982-chr9:86615279..86618286,3	MCF-7	breast:
3	chr9:86591784..86594593-chr9:86615080..86617592,2	MCF-7	breast:
4	chr9:86599801..86602585-chr9:86615309..86617946,2	K562	blood:
5	chr9:86612231..86616038-chr9:86617136..86619825,3	K562	blood:

Variant related genes	Relation type
ENSG00000165119	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10114889	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10115699	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10780640	0.82[AFR][1000 genomes]
rs10868070	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10868071	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10868076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10868080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11140265	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11140289	0.82[EUR][1000 genomes]
rs11140304	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12682981	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13290882	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs13296528	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs167203	0.87[CEU][hapmap]
rs1831757	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs1889113	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2576362	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2780103	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs296883	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs296886	0.87[CEU][hapmap];0.83[TSI][hapmap]
rs296887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs296888	0.89[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs296889	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs296890	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs296892	0.89[YRI][hapmap]
rs296893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs296894	0.81[CEU][hapmap]
rs3180887	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap]
rs3818725	0.88[CHB][hapmap]
rs4147132	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4147133	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4535826	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs4877814	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs4877815	0.86[YRI][hapmap]
rs6559751	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6559752	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6559753	0.89[YRI][hapmap]
rs6559756	0.84[LWK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs696825	0.88[EUR][1000 genomes]
rs7020300	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7021189	0.89[YRI][hapmap]
rs7033292	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7045126	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7853254	0.85[EUR][1000 genomes]
rs7853377	0.87[CEU][hapmap]
rs7869321	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7875011	0.89[YRI][hapmap]
rs796003	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs796004	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs796007	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930340	0.80[CEU][hapmap]
rs9410888	0.88[CHB][hapmap]
rs963459	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv3328820	chr9:86613612-86634313	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1982151	C9orf64	cis	parietal	SCAN
rs1982151	LOC440173	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
2	chr9:86596600-86618200	Weak transcription	Ovary	ovary
3	chr9:86596600-86619600	Weak transcription	Gastric	stomach
4	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
5	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:86597000-86621200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:86597000-86621600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:86597200-86619000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:86597400-86628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:86598800-86622400	Weak transcription	Brain Germinal Matrix	brain
12	chr9:86602000-86620800	Weak transcription	NHLF	lung
13	chr9:86602000-86623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:86602200-86617400	Weak transcription	Osteobl	bone
15	chr9:86602200-86618000	Weak transcription	NHEK	skin
16	chr9:86602200-86618200	Weak transcription	Placenta	Placenta
17	chr9:86602400-86618000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr9:86602400-86627200	Weak transcription	Left Ventricle	heart
19	chr9:86602600-86620000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:86602800-86617400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:86603600-86619600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:86603800-86621200	Weak transcription	Hela-S3	cervix
23	chr9:86604000-86622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:86604000-86626200	Weak transcription	Pancreas	Pancrea
25	chr9:86604200-86618200	Weak transcription	HMEC	breast
26	chr9:86604200-86621400	Weak transcription	Thymus	Thymus
27	chr9:86604200-86623400	Weak transcription	Fetal Stomach	stomach
28	chr9:86605000-86622400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:86605200-86620600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:86605400-86618200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:86605400-86622200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:86606000-86624200	Weak transcription	Fetal Muscle Leg	muscle
33	chr9:86607400-86619400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:86607800-86622600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:86607800-86622800	Weak transcription	K562	blood
36	chr9:86611000-86623000	Weak transcription	Psoas Muscle	Psoas
37	chr9:86611200-86619800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:86613200-86621200	Weak transcription	Adipose Nuclei	Adipose
39	chr9:86614000-86619400	Weak transcription	Fetal Intestine Small	intestine
40	chr9:86614200-86617600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:86614200-86617800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:86614200-86618400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr9:86614200-86618800	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:86614400-86618200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:86614600-86617400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:86614800-86617600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:86615000-86618400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:86615200-86617600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:86615400-86617600	Strong transcription	HUVEC	blood vessel
50	chr9:86615400-86617600	Strong transcription	NHDF-Ad	bronchial

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