Variant report

Variant	rs12554043
Chromosome Location	chr9:97693322-97693323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97692108..97695032-chr9:97695709..97697990,2	K562	blood:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97692349..97695282-chr9:97736142..97738350,2	MCF-7	breast:
4	chr9:97692878..97695081-chr9:97763307..97765405,2	MCF-7	breast:
5	chr9:97692662..97695864-chr9:97697611..97701164,3	K562	blood:
6	chr9:97692662..97694714-chr9:97698664..97701164,2	K562	blood:

Variant related genes	Relation type
ENSG00000224764	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1004813	1.00[JPT][hapmap]
rs10125566	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10217441	1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs10512252	1.00[JPT][hapmap]
rs10732407	0.84[AMR][1000 genomes]
rs10739988	0.84[AMR][1000 genomes]
rs10739990	0.84[AMR][1000 genomes]
rs10739991	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10761362	0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs10821411	0.84[AMR][1000 genomes]
rs10993435	1.00[CEU][hapmap]
rs10993449	1.00[CEU][hapmap]
rs1113967	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12551506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12552838	1.00[AMR][1000 genomes]
rs12555128	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12682668	1.00[JPT][hapmap]
rs12683896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12684072	1.00[JPT][hapmap]
rs12684139	1.00[JPT][hapmap]
rs12684154	1.00[JPT][hapmap]
rs12684461	1.00[JPT][hapmap]
rs12684470	1.00[JPT][hapmap]
rs12684781	1.00[JPT][hapmap]
rs12686277	1.00[JPT][hapmap]
rs12686500	1.00[JPT][hapmap]
rs1382411	0.88[AMR][1000 genomes]
rs1382412	0.88[AMR][1000 genomes]
rs1530331	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs1542107	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1571897	0.87[GIH][hapmap];0.82[JPT][hapmap]
rs16905557	1.00[JPT][hapmap]
rs16911801	1.00[JPT][hapmap]
rs16911802	1.00[JPT][hapmap]
rs16911817	1.00[JPT][hapmap]
rs16911820	1.00[JPT][hapmap]
rs16911821	1.00[JPT][hapmap]
rs16911826	1.00[JPT][hapmap]
rs16911834	1.00[AMR][1000 genomes]
rs16911856	0.80[AMR][1000 genomes]
rs1806996	1.00[JPT][hapmap]
rs1904201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2026399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2061799	0.81[GIH][hapmap]
rs2078379	1.00[JPT][hapmap]
rs2095069	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2119953	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2165715	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs2406897	0.84[AMR][1000 genomes]
rs2406898	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs2584805	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2896816	1.00[CEU][hapmap]
rs2897523	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs356148	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs3824493	1.00[JPT][hapmap]
rs3847309	1.00[JPT][hapmap]
rs3847310	1.00[JPT][hapmap]
rs3847311	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3886567	1.00[JPT][hapmap]
rs3886568	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3887267	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs41316526	0.88[AMR][1000 genomes]
rs4332191	0.84[AMR][1000 genomes]
rs438742	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs456276	0.85[TSI][hapmap]
rs4743976	0.81[GIH][hapmap];0.82[JPT][hapmap]
rs4744389	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs6479568	1.00[JPT][hapmap]
rs6479576	1.00[JPT][hapmap]
rs6479578	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs6479581	0.84[AMR][1000 genomes]
rs66642068	0.88[AMR][1000 genomes]
rs66863985	0.88[AMR][1000 genomes]
rs66993340	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67490803	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67756624	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7019602	1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes]
rs7022739	0.81[GIH][hapmap]
rs7022963	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs7025934	1.00[JPT][hapmap]
rs7026714	1.00[JPT][hapmap]
rs7029570	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7035166	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7038519	1.00[JPT][hapmap]
rs7038891	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7042271	1.00[CEU][hapmap]
rs7044371	0.84[AMR][1000 genomes]
rs7045005	1.00[JPT][hapmap]
rs7046900	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72748601	1.00[AMR][1000 genomes]
rs72750306	0.82[AFR][1000 genomes]
rs73538177	0.88[AMR][1000 genomes]
rs7465900	1.00[JPT][hapmap]
rs7850601	1.00[JPT][hapmap]
rs7850680	1.00[JPT][hapmap]
rs7852844	0.89[ASN][1000 genomes]
rs7867856	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs7869736	0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7870679	1.00[JPT][hapmap]
rs894426	0.84[AMR][1000 genomes]
rs894427	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs894428	1.00[JPT][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12554043	C9orf130	cis	lymphoblastoid	seeQTL
rs12554043	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 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	chr9:97684200-97699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:97684800-97711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:97685200-97714600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr9:97685600-97699600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:97685800-97693600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:97686000-97698800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:97686200-97694200	Genic enhancers	A549	lung
13	chr9:97686400-97695200	Weak transcription	Ovary	ovary
14	chr9:97687000-97693800	Enhancers	HepG2	liver
15	chr9:97687000-97699400	Weak transcription	Fetal Heart	heart
16	chr9:97687000-97714000	Weak transcription	Thymus	Thymus
17	chr9:97687200-97694400	Strong transcription	HSMM	muscle
18	chr9:97688400-97693400	Enhancers	Adipose Nuclei	Adipose
19	chr9:97688800-97694600	Enhancers	Hela-S3	cervix
20	chr9:97689000-97695200	Weak transcription	Aorta	Aorta
21	chr9:97689000-97699400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:97689200-97699600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:97689400-97693400	Enhancers	NHDF-Ad	bronchial
24	chr9:97689600-97693600	Enhancers	Left Ventricle	heart
25	chr9:97689800-97695200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr9:97689800-97697200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr9:97689800-97702600	Weak transcription	Fetal Intestine Large	intestine
28	chr9:97690000-97693800	Weak transcription	K562	blood
29	chr9:97690600-97693400	Enhancers	HUVEC	blood vessel
30	chr9:97690600-97699600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:97690800-97695000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:97691000-97695400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:97691200-97693400	Enhancers	Right Atrium	heart
34	chr9:97691400-97693400	Enhancers	Lung	lung
35	chr9:97691400-97698400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:97691400-97703400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:97691600-97694600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:97691600-97695200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:97691600-97695200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:97691600-97698400	Weak transcription	NHLF	lung
41	chr9:97691600-97699400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:97691800-97693400	Enhancers	Gastric	stomach
43	chr9:97691800-97696800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr9:97691800-97698200	Weak transcription	Fetal Lung	lung
45	chr9:97691800-97710800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:97692000-97693400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr9:97692000-97699000	Weak transcription	Brain Anterior Caudate	brain
48	chr9:97692200-97693400	Enhancers	Colonic Mucosa	Colon
49	chr9:97692200-97695200	Weak transcription	Osteobl	bone
50	chr9:97692200-97713000	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links