Variant report

Variant	rs12344211
Chromosome Location	chr9:97691104-97691105
allele	C/T
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97688635..97691116-chr9:97722109..97725030,2	MCF-7	breast:
4	chr9:97688920..97691846-chr9:97741162..97743776,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FANCC-1	chr9:97690833-97691145	ENSG00000224764.1
2	lnc-FANCC-1	chr9:97691050-97691145	NONHSAT133341

No data

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10081676	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10217143	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10761361	0.85[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10821410	0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10821413	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993387	0.81[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12338409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12338859	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12347649	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16911824	0.83[YRI][hapmap]
rs1867102	0.80[CHB][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap]
rs4743969	0.88[MKK][hapmap];0.84[TSI][hapmap]
rs4743974	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4744386	0.88[MKK][hapmap];0.84[TSI][hapmap]
rs4744412	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7847277	0.89[MKK][hapmap];0.84[TSI][hapmap]
rs7848139	0.88[MKK][hapmap];0.84[TSI][hapmap]
rs7862219	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7870160	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9802263	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1045849	chr9:97688810-97741336	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr9:97680400-97698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:97680600-97700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr9:97682000-97713800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr9:97682200-97691200	Enhancers	Placenta	Placenta
7	chr9:97684200-97699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:97684800-97711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:97685200-97693000	Weak transcription	Small Intestine	intestine
10	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:97685600-97699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:97685800-97693600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:97686000-97691400	Weak transcription	Spleen	Spleen
14	chr9:97686000-97698800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:97686200-97694200	Genic enhancers	A549	lung
16	chr9:97686400-97691600	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:97686400-97695200	Weak transcription	Ovary	ovary
18	chr9:97686600-97691200	Weak transcription	Right Atrium	heart
19	chr9:97686800-97691800	Weak transcription	Brain Germinal Matrix	brain
20	chr9:97687000-97693800	Enhancers	HepG2	liver
21	chr9:97687000-97699400	Weak transcription	Fetal Heart	heart
22	chr9:97687000-97714000	Weak transcription	Thymus	Thymus
23	chr9:97687200-97691400	Strong transcription	Fetal Stomach	stomach
24	chr9:97687200-97694400	Strong transcription	HSMM	muscle
25	chr9:97687400-97692800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr9:97687600-97692200	Strong transcription	HSMMtube	muscle
27	chr9:97687600-97693000	Strong transcription	Fetal Intestine Small	intestine
28	chr9:97687800-97692000	Enhancers	Stomach Mucosa	stomach
29	chr9:97687800-97692600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:97688400-97693400	Enhancers	Adipose Nuclei	Adipose
31	chr9:97688800-97693200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:97688800-97694600	Enhancers	Hela-S3	cervix
33	chr9:97689000-97695200	Weak transcription	Aorta	Aorta
34	chr9:97689000-97699400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:97689200-97691800	Weak transcription	Gastric	stomach
36	chr9:97689200-97699600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:97689400-97692200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr9:97689400-97693400	Enhancers	NHDF-Ad	bronchial
39	chr9:97689600-97692200	Enhancers	Brain Cingulate Gyrus	brain
40	chr9:97689600-97693000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr9:97689600-97693600	Enhancers	Left Ventricle	heart
42	chr9:97689800-97691400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:97689800-97691600	Enhancers	NHLF	lung
44	chr9:97689800-97692400	Enhancers	Fetal Muscle Trunk	muscle
45	chr9:97689800-97692600	Enhancers	NH-A	brain
46	chr9:97689800-97695200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:97689800-97697200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr9:97689800-97702600	Weak transcription	Fetal Intestine Large	intestine
49	chr9:97690000-97691600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:97690000-97691600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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