Variant report

Variant	rs10464287
Chromosome Location	chr7:16459659-16459660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16441426..16443801-chr7:16458658..16460792,2	K562	blood:
2	chr7:16302626..16306339-chr7:16456665..16460333,5	K562	blood:
3	chr7:16456001..16461931-chr7:16682283..16687700,6	K562	blood:
4	chr7:16302978..16309646-chr7:16456908..16462647,13	K562	blood:

Variant related genes	Relation type
ENSG00000229688	Chromatin interaction
ENSG00000106524	Chromatin interaction
ENSG00000136261	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10257504	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10950619	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11976934	0.87[EUR][1000 genomes]
rs17617900	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17680292	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28512480	0.85[EUR][1000 genomes]
rs56206818	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56223703	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56335840	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60989361	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6461255	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66743577	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6947550	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6948660	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6949112	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6955398	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6958802	0.96[CEU][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7457079	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782939	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9655136	0.81[CEU][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9691296	0.80[AMR][1000 genomes];0.88[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	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2759514	chr7:16236162-16527390	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758105	chr7:16272822-16527390	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1034151	chr7:16415497-16578081	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10464287	SNX13	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16450600-16459800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:16453000-16460400	Weak transcription	Gastric	stomach
3	chr7:16455800-16459800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:16456400-16459800	Weak transcription	Lung	lung
5	chr7:16456600-16459800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:16457200-16459800	Weak transcription	NHLF	lung
7	chr7:16457400-16459800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:16457400-16459800	Weak transcription	NH-A	brain
9	chr7:16457800-16459800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:16457800-16459800	Weak transcription	HSMM	muscle
11	chr7:16457800-16459800	Weak transcription	HSMMtube	muscle
12	chr7:16457800-16459800	Weak transcription	NHDF-Ad	bronchial
13	chr7:16458600-16459800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:16458800-16459800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:16459000-16459800	Enhancers	Stomach Mucosa	stomach
16	chr7:16459400-16459800	Enhancers	Primary T cells from cord blood	blood
17	chr7:16459400-16459800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr7:16459400-16459800	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr7:16459400-16459800	Enhancers	Colon Smooth Muscle	Colon
20	chr7:16459400-16459800	Enhancers	Fetal Heart	heart
21	chr7:16459400-16459800	Enhancers	Fetal Intestine Large	intestine
22	chr7:16459400-16461400	Active TSS	K562	blood
23	chr7:16459600-16459800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
24	chr7:16459600-16459800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr7:16459600-16459800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr7:16459600-16459800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
27	chr7:16459600-16459800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:16459600-16459800	Enhancers	Primary B cells from cord blood	blood
29	chr7:16459600-16459800	Enhancers	Primary B cells from peripheral blood	blood
30	chr7:16459600-16459800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr7:16459600-16459800	Enhancers	Primary hematopoietic stem cells	blood
32	chr7:16459600-16459800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr7:16459600-16459800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr7:16459600-16459800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:16459600-16459800	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr7:16459600-16459800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:16459600-16459800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr7:16459600-16459800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:16459600-16459800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:16459600-16459800	Enhancers	Adipose Nuclei	Adipose
41	chr7:16459600-16459800	Enhancers	Liver	Liver
42	chr7:16459600-16459800	Enhancers	Brain Cingulate Gyrus	brain
43	chr7:16459600-16459800	Enhancers	Brain Hippocampus Middle	brain
44	chr7:16459600-16459800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr7:16459600-16459800	Enhancers	Brain Substantia Nigra	brain
46	chr7:16459600-16459800	Enhancers	Colonic Mucosa	Colon
47	chr7:16459600-16459800	Enhancers	Fetal Brain Male	brain
48	chr7:16459600-16459800	Enhancers	Fetal Brain Female	brain
49	chr7:16459600-16459800	Enhancers	Fetal Lung	lung
50	chr7:16459600-16459800	Enhancers	Fetal Muscle Trunk	muscle

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