Variant report

Variant	rs4430500
Chromosome Location	chr11:10254371-10254372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10253231..10255912-chr11:10256898..10258938,2	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10500724	0.85[CEU][hapmap]
rs10770100	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840378	0.85[CHD][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11042682	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042685	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042702	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs11042714	0.82[CEU][hapmap]
rs1114426	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11607174	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs11607447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12281432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372811	0.85[CEU][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1442739	0.86[ASN][1000 genomes]
rs1442740	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1450271	0.82[ASN][1000 genomes]
rs1470259	0.86[ASN][1000 genomes]
rs1470260	0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs1562782	1.00[ASW][hapmap]
rs1822293	1.00[ASW][hapmap];0.85[CEU][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1837978	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1988724	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2015148	0.82[ASN][1000 genomes]
rs2083714	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084600	0.82[ASN][1000 genomes]
rs2197170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2218305	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2403291	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2920150	0.86[ASN][1000 genomes]
rs2920151	0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs2920152	0.86[ASN][1000 genomes]
rs2923089	0.82[ASN][1000 genomes]
rs2957683	0.82[ASN][1000 genomes]
rs4258371	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4323860	0.82[CEU][hapmap]
rs4534577	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4550215	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4553358	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597056	0.82[CEU][hapmap]
rs4612801	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4909923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910100	0.81[EUR][1000 genomes]
rs4910101	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4910102	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4910104	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910108	0.81[YRI][hapmap]
rs4910109	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910112	0.86[ASN][1000 genomes]
rs4910113	0.86[ASN][1000 genomes]
rs4910114	0.86[ASN][1000 genomes]
rs4910115	0.82[CEU][hapmap]
rs4910116	0.86[ASN][1000 genomes]
rs55879783	0.86[ASN][1000 genomes]
rs56035322	0.86[ASN][1000 genomes]
rs56352102	0.86[ASN][1000 genomes]
rs57975523	0.86[ASN][1000 genomes]
rs59033026	0.86[ASN][1000 genomes]
rs59090117	0.86[ASN][1000 genomes]
rs59807815	0.86[ASN][1000 genomes]
rs61889814	0.86[ASN][1000 genomes]
rs6484147	0.82[CEU][hapmap]
rs6484152	0.82[CEU][hapmap]
rs7108358	0.81[CEU][hapmap]
rs7110652	0.81[CEU][hapmap]
rs7112413	0.86[ASN][1000 genomes]
rs7117478	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118500	0.81[CEU][hapmap]
rs7122026	0.82[AMR][1000 genomes]
rs7123728	0.82[CEU][hapmap]
rs716804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73419149	0.86[ASN][1000 genomes]
rs7479039	0.81[CEU][hapmap]
rs7926490	0.82[ASN][1000 genomes]
rs7937758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938543	0.85[CEU][hapmap]
rs7941312	0.82[ASN][1000 genomes]
rs7941511	0.86[ASN][1000 genomes]
rs7947059	0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs7947666	0.82[CEU][hapmap]
rs9704692	0.82[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	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1039636	chr11:10126747-10280570	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4430500	SYT9	cis	cerebellum	SCAN
rs4430500	TRIM66	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10231000-10254400	Weak transcription	NHDF-Ad	bronchial
2	chr11:10231000-10254400	Weak transcription	NHLF	lung
3	chr11:10235400-10263400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr11:10240600-10259800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:10241200-10255200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:10241800-10254800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:10247800-10255200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:10247800-10259200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:10252000-10255200	Weak transcription	Osteobl	bone
10	chr11:10252200-10264200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:10252600-10254800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr11:10252600-10255000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:10253000-10254800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:10253000-10268200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr11:10253200-10254400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:10253400-10254400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:10253400-10254400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
18	chr11:10253400-10254400	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr11:10253400-10255000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:10253600-10254600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:10253600-10254800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
22	chr11:10253800-10254400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
23	chr11:10253800-10254400	Weak transcription	Adipose Nuclei	Adipose
24	chr11:10253800-10254600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
25	chr11:10253800-10254600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:10253800-10256600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr11:10253800-10256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:10254000-10255200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr11:10254000-10255200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr11:10254000-10255600	Enhancers	Primary hematopoietic stem cells	blood
31	chr11:10254000-10258800	Weak transcription	Left Ventricle	heart
32	chr11:10254000-10259800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:10254000-10263400	Weak transcription	Ovary	ovary
34	chr11:10254000-10276200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:10254200-10256000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links