Variant report

Variant	rs7870926
Chromosome Location	chr9:100796945-100796946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100684268..100684829-chr9:100796846..100797760,2	K562	blood:
2	chr9:100684661..100686943-chr9:100794140..100799259,5	K562	blood:
3	chr9:100685383..100686650-chr9:100796663..100797820,11	K562	blood:
4	chr9:100744061..100747104-chr9:100795931..100798859,4	MCF-7	breast:
5	chr9:100685498..100686359-chr9:100796718..100798043,9	MCF-7	breast:
6	chr9:100793900..100798932-chr9:100816820..100821233,8	MCF-7	breast:
7	chr9:100796342..100798790-chr9:101837762..101839571,2	K562	blood:
8	chr9:100796501..100799835-chr9:100807798..100809968,3	K562	blood:
9	chr9:100789228..100794108-chr9:100794751..100799924,8	K562	blood:
10	chr9:100685785..100686517-chr9:100796418..100797247,3	MCF-7	breast:
11	chr9:100776438..100779728-chr9:100795602..100798720,4	K562	blood:
12	chr9:100705623..100707205-chr9:100796922..100798794,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000136929	Chromatin interaction
ENSG00000136932	Chromatin interaction
ENSG00000136938	Chromatin interaction
ENSG00000095380	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1010777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10116946	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10125654	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984606	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1131641	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1572025	0.81[GIH][hapmap]
rs3739672	0.81[GIH][hapmap]
rs4742710	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743152	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56145417	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7035650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7044744	0.89[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7855088	0.81[GIH][hapmap]
rs7874518	0.96[EUR][1000 genomes]
rs987142	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[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	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv3493282	chr9:100784615-100805700	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3493283	chr9:100784615-100805700	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7870926	C9orf102	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100782400-100797000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:100783600-100797000	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100783800-100797000	Weak transcription	NHEK	skin
4	chr9:100784000-100803800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr9:100784200-100797000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:100784400-100797000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:100784400-100797000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:100784400-100797400	Weak transcription	HSMMtube	muscle
9	chr9:100785000-100797000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:100785000-100801400	Weak transcription	Fetal Intestine Small	intestine
11	chr9:100785200-100797400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:100785600-100797000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:100789200-100797000	Weak transcription	Thymus	Thymus
14	chr9:100794400-100797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:100794400-100797400	Weak transcription	NHLF	lung
16	chr9:100794800-100797000	Weak transcription	NH-A	brain
17	chr9:100795000-100797000	Weak transcription	NHDF-Ad	bronchial
18	chr9:100795200-100797000	Weak transcription	Osteobl	bone
19	chr9:100795400-100797200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:100795600-100800200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:100796000-100797200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr9:100796600-100797000	Weak transcription	Colonic Mucosa	Colon
23	chr9:100796600-100797200	Enhancers	Fetal Thymus	thymus
24	chr9:100796800-100797000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr9:100796800-100797000	Active TSS	Primary hematopoietic stem cells	blood
26	chr9:100796800-100797000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr9:100796800-100797000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:100796800-100797000	Active TSS	Brain Anterior Caudate	brain
29	chr9:100796800-100797000	Weak transcription	Brain Germinal Matrix	brain
30	chr9:100796800-100797000	Active TSS	Brain Hippocampus Middle	brain
31	chr9:100796800-100797000	Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr9:100796800-100797000	Active TSS	Stomach Smooth Muscle	stomach
33	chr9:100796800-100797000	Flanking Active TSS	A549	lung
34	chr9:100796800-100797200	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr9:100796800-100797200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr9:100796800-100797200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr9:100796800-100797200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr9:100796800-100797200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr9:100796800-100797200	Enhancers	Brain Cingulate Gyrus	brain
40	chr9:100796800-100797200	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr9:100796800-100797200	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr9:100796800-100797200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr9:100796800-100797200	Enhancers	Gastric	stomach
44	chr9:100796800-100797200	Enhancers	Pancreas	Pancrea
45	chr9:100796800-100797200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr9:100796800-100797200	Active TSS	Rectal Smooth Muscle	rectum
47	chr9:100796800-100797200	Enhancers	Right Atrium	heart
48	chr9:100796800-100797200	Flanking Active TSS	Hela-S3	cervix
49	chr9:100796800-100797200	Flanking Active TSS	HepG2	liver
50	chr9:100796800-100797400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links