Variant report

Variant	rs11730667
Chromosome Location	chr4:74600211-74600212
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:74596146..74598686-chr4:74599662..74602190,5	K562	blood:
2	chr4:74591810..74594488-chr4:74595060..74600715,5	MCF-7	breast:
3	chr4:74596146..74597922-chr4:74599662..74601519,2	K562	blood:
4	chr4:74572825..74575404-chr4:74599407..74602314,2	K562	blood:
5	chr4:74588963..74591805-chr4:74598001..74600687,2	MCF-7	breast:
6	chr4:74599752..74603059-chr4:74603100..74608923,6	K562	blood:

Variant related genes	Relation type
ENSG00000169429	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10005565	0.92[ASN][1000 genomes]
rs10009462	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10009488	0.93[ASN][1000 genomes]
rs10010970	0.92[ASN][1000 genomes]
rs10012962	0.83[ASN][1000 genomes]
rs10015626	0.92[ASN][1000 genomes]
rs10019318	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10031141	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs10938092	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10938094	0.84[ASN][1000 genomes]
rs10938095	0.84[ASN][1000 genomes]
rs10938096	0.81[ASN][1000 genomes]
rs10938097	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10938100	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1126647	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11730284	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730560	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11938389	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12503139	0.81[ASN][1000 genomes]
rs12644561	0.81[ASN][1000 genomes]
rs13106097	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13109146	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13109377	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112910	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13116536	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13117876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151869	0.81[ASN][1000 genomes]
rs16849928	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849945	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16849958	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951235	0.82[ASN][1000 genomes]
rs1951236	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951240	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1957070	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1957661	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2145617	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2224434	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2227306	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2227307	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227521	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227543	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2367276	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28609798	0.84[ASN][1000 genomes]
rs28612337	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2886920	0.92[ASN][1000 genomes]
rs2886922	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4073	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4279174	0.83[ASN][1000 genomes]
rs4549349	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4694178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694639	0.85[CHB][hapmap]
rs62312370	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6446959	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446960	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6446961	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs6820848	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6853679	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7689435	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9999262	0.83[ASN][1000 genomes]
rs9999446	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1008104	chr4:74468434-74621952	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012198	chr4:74487793-74621952	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv537139	chr4:74487793-74621952	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1005231	chr4:74555497-74680079	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11730667	PF4V1	cis	multi-tissue	Pritchard
rs11730667	ALB	cis	cerebellum	SCAN
rs11730667	SDAD1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74595000-74602400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr4:74595200-74601800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr4:74596200-74600400	Weak transcription	HMEC	breast
4	chr4:74596400-74600400	Weak transcription	A549	lung
5	chr4:74596400-74600600	Weak transcription	NHEK	skin
6	chr4:74596400-74605400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:74596400-74606000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:74597000-74600600	Weak transcription	Hela-S3	cervix
9	chr4:74597400-74601400	Weak transcription	Lung	lung
10	chr4:74597800-74601800	Enhancers	HUVEC	blood vessel
11	chr4:74598000-74605200	Weak transcription	Left Ventricle	heart
12	chr4:74598400-74602000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr4:74598400-74602200	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr4:74598800-74601600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:74599000-74601600	Enhancers	GM12878-XiMat	blood
16	chr4:74599600-74600400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:74599800-74600400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:74599800-74600400	Bivalent Enhancer	Adipose Nuclei	Adipose
19	chr4:74599800-74600600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:74599800-74600800	Enhancers	Colon Smooth Muscle	Colon
21	chr4:74599800-74602000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:74600000-74600400	Enhancers	Ovary	ovary
23	chr4:74600000-74600400	Flanking Active TSS	NHDF-Ad	bronchial
24	chr4:74600000-74600600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr4:74600000-74600600	Enhancers	HSMM	muscle
26	chr4:74600000-74601000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:74600000-74601000	Enhancers	K562	blood
28	chr4:74600000-74601200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:74600000-74601200	Enhancers	NHLF	lung
30	chr4:74600000-74601400	Enhancers	Osteobl	bone
31	chr4:74600000-74601600	Enhancers	Primary hematopoietic stem cells	blood
32	chr4:74600000-74601600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:74600200-74600400	Enhancers	Primary B cells from cord blood	blood
34	chr4:74600200-74600400	Enhancers	Small Intestine	intestine
35	chr4:74600200-74600600	Enhancers	HSMMtube	muscle
36	chr4:74600200-74600800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:74600200-74600800	Enhancers	NH-A	brain
38	chr4:74600200-74601200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links