Variant report

Variant	rs9535292
Chromosome Location	chr13:50244041-50244042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50242666..50244239-chr13:50569416..50571466,2	MCF-7	breast:
2	chr13:50243856..50246257-chr13:50421112..50423233,2	MCF-7	breast:
3	chr13:50243658..50244532-chr13:50421679..50422537,5	MCF-7	breast:
4	chr13:50242498..50244504-chr13:50366051..50367551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264864	Chromatin interaction
ENSG00000102753	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13313256	0.85[JPT][hapmap]
rs1535470	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs1535544	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs1570407	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885539	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407797	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3903768	0.86[JPT][hapmap]
rs61959934	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61959936	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7319110	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325692	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7327024	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737250	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737251	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316473	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs942030	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942031	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526590	0.84[EUR][1000 genomes]
rs9535296	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535297	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535299	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568303	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568304	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568305	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9591296	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9535292	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs9535292	KCNRG	cis	cerebellum	SCAN
rs9535292	RCBTB1	cis	cerebellum	SCAN
rs9535292	TRIM13	cis	cerebellum	SCAN
rs9535292	HTR2A	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50220000-50245400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr13:50224600-50252600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50227400-50253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:50231000-50246800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr13:50231800-50256000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr13:50234400-50245400	Weak transcription	Psoas Muscle	Psoas
7	chr13:50235400-50252400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:50235600-50259800	Weak transcription	Right Ventricle	heart
9	chr13:50237000-50256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr13:50237400-50256000	Weak transcription	NH-A	brain
11	chr13:50238800-50253000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr13:50240600-50253400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr13:50240800-50244200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr13:50240800-50246400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
16	chr13:50241600-50245800	Weak transcription	Hela-S3	cervix
17	chr13:50241600-50249800	Weak transcription	GM12878-XiMat	blood
18	chr13:50241800-50253400	Weak transcription	Esophagus	oesophagus
19	chr13:50241800-50256000	Weak transcription	HMEC	breast
20	chr13:50242000-50244400	Weak transcription	Fetal Brain Male	brain
21	chr13:50242000-50254000	Weak transcription	Fetal Brain Female	brain
22	chr13:50242200-50244200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:50242200-50244400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:50242200-50245200	Weak transcription	Ovary	ovary
25	chr13:50242200-50246000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr13:50242200-50246200	Weak transcription	Placenta	Placenta
27	chr13:50242200-50249000	Weak transcription	NHEK	skin
28	chr13:50242200-50251200	Weak transcription	Pancreas	Pancrea
29	chr13:50242200-50251200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr13:50242200-50251400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr13:50242200-50252000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:50242200-50253000	Weak transcription	Fetal Thymus	thymus
33	chr13:50242200-50253400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:50242200-50256200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:50242200-50260600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr13:50242200-50264200	Weak transcription	K562	blood
39	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr13:50242400-50244200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr13:50242400-50244200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr13:50242400-50244200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr13:50242400-50244200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr13:50242400-50244200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:50242400-50244200	Weak transcription	NHDF-Ad	bronchial
47	chr13:50242400-50244600	Weak transcription	Liver	Liver
48	chr13:50242400-50244800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr13:50242400-50245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr13:50242400-50245000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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