Variant report

Variant	rs472518
Chromosome Location	chr11:65851902-65851903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65850193..65852902-chr11:66111593..66113196,2	MCF-7	breast:
2	chr11:65849463..65852379-chr11:66024191..66026545,2	K562	blood:
3	chr1:145381411..145383817-chr11:65849842..65852203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233396	Chromatin interaction
ENSG00000174996	Chromatin interaction
ENSG00000174744	Chromatin interaction
ENSG00000201558	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1055615	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10791853	0.83[ASN][1000 genomes]
rs10791856	0.81[ASN][1000 genomes]
rs10896081	0.81[EUR][1000 genomes]
rs10896085	0.81[EUR][1000 genomes]
rs10896087	0.81[EUR][1000 genomes]
rs10896092	0.83[ASN][1000 genomes]
rs10896097	0.81[ASN][1000 genomes]
rs11227411	0.81[EUR][1000 genomes]
rs11227413	0.81[EUR][1000 genomes]
rs11227414	0.81[EUR][1000 genomes]
rs11227415	0.81[EUR][1000 genomes]
rs11227426	0.82[ASN][1000 genomes]
rs12049852	0.86[ASN][1000 genomes]
rs1717671	0.83[ASN][1000 genomes]
rs1987678	0.87[ASN][1000 genomes]
rs3088328	0.93[ASN][1000 genomes]
rs4013917	0.81[EUR][1000 genomes]
rs471484	0.83[ASN][1000 genomes]
rs475805	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs485857	0.83[ASN][1000 genomes]
rs488320	0.85[ASN][1000 genomes]
rs489337	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap]
rs524281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs535395	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs537497	0.87[GIH][hapmap]
rs539046	0.81[GIH][hapmap]
rs547087	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs564343	0.87[GIH][hapmap]
rs565198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs571434	0.85[ASN][1000 genomes]
rs7115081	0.80[EUR][1000 genomes]
rs7926402	0.81[EUR][1000 genomes]
rs7931544	0.81[EUR][1000 genomes]
rs7937281	0.84[ASN][1000 genomes]
rs7941469	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs918299	0.81[EUR][1000 genomes]
rs9645684	0.81[EUR][1000 genomes]
rs9736673	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs472518	WDR74	cis	cerebellum	SCAN
rs472518	KLC2	cis	Muscle Skeletal	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65839600-65854600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:65840600-65870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:65842200-65867800	Weak transcription	Ovary	ovary
4	chr11:65845200-65854400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr11:65845800-65868800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:65846200-65853600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr11:65847200-65852000	Enhancers	Duodenum Mucosa	Duodenum
8	chr11:65847600-65852000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:65847600-65852000	Enhancers	HUVEC	blood vessel
10	chr11:65847600-65852800	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr11:65847600-65852800	Enhancers	Osteobl	bone
12	chr11:65847600-65853000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr11:65848000-65854800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:65848400-65874200	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:65849000-65853600	Enhancers	Fetal Heart	heart
16	chr11:65849200-65852200	Enhancers	Hela-S3	cervix
17	chr11:65849200-65853400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:65849200-65879600	Weak transcription	Aorta	Aorta
19	chr11:65849400-65852000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:65849400-65854600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:65849400-65856200	Enhancers	Primary T cells fromperipheralblood	blood
22	chr11:65849400-65858000	Enhancers	Primary B cells from peripheral blood	blood
23	chr11:65849400-65858800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:65849600-65852000	Enhancers	Fetal Thymus	thymus
25	chr11:65849600-65853400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:65849600-65856800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr11:65849600-65857000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:65849600-65858600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr11:65849800-65853000	Enhancers	Primary hematopoietic stem cells	blood
30	chr11:65849800-65857800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr11:65849800-65858200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:65849800-65867600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:65850000-65852400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr11:65850000-65855800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr11:65850200-65866200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr11:65850400-65852000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:65850400-65852000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:65850400-65852200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr11:65850400-65852200	Enhancers	HepG2	liver
40	chr11:65850600-65852000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr11:65850600-65852000	Flanking Active TSS	A549	lung
42	chr11:65850600-65852400	Enhancers	Brain Anterior Caudate	brain
43	chr11:65850800-65852000	Enhancers	Stomach Mucosa	stomach
44	chr11:65850800-65852200	Enhancers	Left Ventricle	heart
45	chr11:65850800-65852200	Enhancers	Right Ventricle	heart
46	chr11:65850800-65852600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr11:65850800-65852800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr11:65850800-65852800	Enhancers	Brain Angular Gyrus	brain
49	chr11:65851000-65852000	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr11:65851000-65852000	Enhancers	Spleen	Spleen

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