Variant report

Variant	rs2071304
Chromosome Location	chr11:47372377-47372378
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47371255..47374235-chr11:47398833..47401671,2	K562	blood:
2	chr11:47289586..47293263-chr11:47367721..47372690,6	MCF-7	breast:
3	chr11:47203691..47205967-chr11:47371684..47373838,2	K562	blood:
4	chr11:47289111..47291815-chr11:47370761..47372968,2	MCF-7	breast:
5	chr11:47183301..47185568-chr11:47370586..47372939,2	K562	blood:
6	chr11:47368613..47373799-chr11:47374584..47376990,4	MCF-7	breast:
7	chr11:47289275..47291603-chr11:47370124..47373215,3	K562	blood:

Variant related genes	Relation type
ENSG00000110514	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000066336	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1057233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10734557	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10742803	1.00[CEU][hapmap]
rs10769258	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10769262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs10838698	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10838699	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838704	0.84[EUR][1000 genomes]
rs10838706	0.80[EUR][1000 genomes]
rs10838708	0.86[CHB][hapmap]
rs11039195	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039199	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039200	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039202	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11039203	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039219	0.81[EUR][1000 genomes]
rs11570094	0.83[CEU][hapmap]
rs11601603	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11604680	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs11605672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs11607981	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12146565	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12802273	0.81[EUR][1000 genomes]
rs12803525	0.82[EUR][1000 genomes]
rs1317149	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs1317164	0.82[EUR][1000 genomes]
rs1542321	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2053979	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs2084946	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293577	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2293578	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[EUR][1000 genomes]
rs2856661	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2868459	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs34958982	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs35996350	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3740686	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740688	0.83[ASN][1000 genomes]
rs3781624	0.81[EUR][1000 genomes]
rs3781625	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes]
rs3781626	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs3781627	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs4752827	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752845	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs4752987	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs4752993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4752994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4752999	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs4992357	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55677087	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55876153	0.82[EUR][1000 genomes]
rs56030824	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58965622	0.83[EUR][1000 genomes]
rs6485753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs67116452	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67472071	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7105851	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7107726	0.82[EUR][1000 genomes]
rs7124681	0.90[CHB][hapmap]
rs755553	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs755554	1.00[CEU][hapmap];0.86[CHB][hapmap]
rs755555	0.83[EUR][1000 genomes]
rs7928163	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7928842	0.95[CHB][hapmap]
rs7937331	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs7940536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs896816	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs935914	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2071304	SPI1	cis	multi-tissue	Pritchard
rs2071304		cis	Lymphoblastoid	GTEx
rs2071304	SPI1	cis	Lymphoblastoid	GTEx
rs2071304	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs2071304	C1QTNF4	cis	Muscle Skeletal	GTEx
rs2071304	C1QTNF4	cis	multi-tissue	Pritchard
rs2071304	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs2071304	Hs.6637	cis	multi-tissue	Pritchard
rs2071304	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47351400-47375600	Weak transcription	Primary B cells from cord blood	blood
2	chr11:47353600-47375400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr11:47354800-47372800	Weak transcription	Gastric	stomach
4	chr11:47367800-47377200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:47368600-47374800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr11:47369600-47372400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:47369800-47374400	Active TSS	Right Atrium	heart
8	chr11:47369800-47375600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr11:47370000-47374800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr11:47370600-47373000	Transcr. at gene 5' and 3'	Right Ventricle	heart
11	chr11:47370800-47377000	Weak transcription	K562	blood
12	chr11:47371000-47373600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:47371000-47379800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr11:47371200-47373000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:47371200-47376200	Weak transcription	Fetal Intestine Small	intestine
16	chr11:47371600-47372400	Weak transcription	Spleen	Spleen
17	chr11:47372000-47372600	Enhancers	Fetal Muscle Leg	muscle
18	chr11:47372000-47374400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
19	chr11:47372000-47374400	Bivalent Enhancer	HepG2	liver
20	chr11:47372200-47372400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:47372200-47372400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:47372200-47372800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr11:47372200-47373000	Transcr. at gene 5' and 3'	Left Ventricle	heart
24	chr11:47372200-47373400	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr11:47372200-47373400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:47372200-47374200	Active TSS	Fetal Heart	heart

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