Variant report

Variant	rs13251032
Chromosome Location	chr8:96099994-96099995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95906412..95908805-chr8:96098165..96100293,2	MCF-7	breast:
2	chr8:96095758..96103345-chr8:96144049..96152228,17	MCF-7	breast:
3	chr8:96097741..96100033-chr8:96272742..96274690,2	MCF-7	breast:
4	chr8:96096484..96101537-chr8:96142870..96147410,9	MCF-7	breast:
5	chr8:96097941..96100243-chr8:97273935..97276169,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TP53INP1-2	chr8:96099874-96100152	ENSG00000254248.1

Variant related genes	Relation type
ENSG00000156170	Chromatin interaction
ENSG00000175305	Chromatin interaction
ENSG00000156471	Chromatin interaction
ENSG00000175895	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1000285	0.82[CHB][hapmap]
rs1000286	0.82[CHB][hapmap]
rs10093559	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs10096848	0.82[CHB][hapmap]
rs11776488	0.82[CHB][hapmap];0.83[GIH][hapmap]
rs11781134	1.00[CHB][hapmap]
rs11781447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11782155	0.82[CHB][hapmap]
rs11784746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12548426	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13248868	0.97[ASN][1000 genomes]
rs13251759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13273307	0.97[ASN][1000 genomes]
rs13274368	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451711	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1451712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1946941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1946943	1.00[ASN][1000 genomes]
rs1946944	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2341400	0.97[ASN][1000 genomes]
rs34901613	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4236831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4321970	0.95[ASN][1000 genomes]
rs4323439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4329243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4540384	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4734298	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4734299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6987762	0.92[ASN][1000 genomes]
rs7008347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv891205	chr8:96062601-96115476	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
5	nsv891206	chr8:96092251-96115476	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13251032	GFRA1	trans	parietal	SCAN
rs13251032	C8orf38	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96080200-96101800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:96097400-96100000	Weak transcription	Esophagus	oesophagus
3	chr8:96097600-96100800	Enhancers	Placenta	Placenta
4	chr8:96098000-96100800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr8:96098000-96100800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr8:96098200-96100200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:96098200-96100800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr8:96098400-96100200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:96098400-96101800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr8:96098400-96102400	Weak transcription	Stomach Mucosa	stomach
11	chr8:96098600-96100000	Weak transcription	Fetal Thymus	thymus
12	chr8:96098600-96100200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:96098600-96101800	Weak transcription	Gastric	stomach
14	chr8:96098600-96101800	Weak transcription	HUVEC	blood vessel
15	chr8:96098600-96102000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr8:96098600-96102200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr8:96098600-96102200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr8:96098600-96102400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr8:96098600-96111600	Weak transcription	Pancreas	Pancrea
20	chr8:96098800-96100000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr8:96098800-96100000	Weak transcription	K562	blood
22	chr8:96098800-96102000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr8:96098800-96102200	Weak transcription	Thymus	Thymus
24	chr8:96098800-96102400	Weak transcription	Dnd41	blood
25	chr8:96098800-96103800	Weak transcription	HepG2	liver
26	chr8:96099000-96100000	Weak transcription	Fetal Muscle Leg	muscle
27	chr8:96099200-96100000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr8:96099200-96100000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr8:96099200-96100000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr8:96099200-96100200	Weak transcription	Lung	lung
31	chr8:96099200-96100600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:96099200-96100800	Enhancers	Primary B cells from peripheral blood	blood
33	chr8:96099400-96100200	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr8:96099400-96100200	Weak transcription	Colonic Mucosa	Colon
35	chr8:96099600-96100400	Enhancers	Duodenum Mucosa	Duodenum
36	chr8:96099600-96100400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr8:96099600-96100400	Flanking Active TSS	NHEK	skin
38	chr8:96099600-96100600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr8:96099600-96101800	Enhancers	GM12878-XiMat	blood
40	chr8:96099800-96100200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr8:96099800-96100400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr8:96099800-96100800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr8:96099800-96100800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr8:96099800-96101600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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