Variant report

Variant	rs10787292
Chromosome Location	chr10:112697241-112697242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:112697078-112697243	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:112697054..112698735-chr10:112706865..112709739,2	K562	blood:
2	chr10:112677485..112680905-chr10:112696350..112700143,5	K562	blood:
3	chr10:112677742..112679922-chr10:112696330..112699215,3	K562	blood:
4	chr10:112673558..112675632-chr10:112697119..112699453,2	K562	blood:

Variant related genes	Relation type
RPL13AP6	TF binding region
ENSG00000108061	Chromatin interaction
ENSG00000214413	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10787287	0.93[ASW][hapmap];0.85[CEU][hapmap];0.81[CHD][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs10787289	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs10885075	0.92[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1327548	0.91[EUR][1000 genomes]
rs1341051	0.91[TSI][hapmap]
rs1359849	0.85[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410054	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1410057	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571239	0.89[YRI][hapmap]
rs1581886	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128202	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1887460	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1927159	0.82[MKK][hapmap]
rs1980869	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs4309090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6421360	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs6585027	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7067540	0.88[TSI][hapmap]
rs7072816	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7075507	0.86[AFR][1000 genomes]
rs7082572	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7088364	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7089193	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7089615	0.81[AFR][1000 genomes]
rs7095404	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7895872	0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7899762	0.89[EUR][1000 genomes]
rs7917192	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7922142	1.00[YRI][hapmap];0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1051327	chr10:112650316-112772917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540774	chr10:112650316-112772917	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1047865	chr10:112660427-112730573	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1048809	chr10:112683822-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv518667	chr10:112692802-112697241	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10787292	XPNPEP1	cis	cerebellum	SCAN
rs10787292	NRAP	cis	parietal	SCAN
rs10787292	HABP2	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112680600-112706800	Weak transcription	Esophagus	oesophagus
2	chr10:112680800-112704600	Weak transcription	Aorta	Aorta
3	chr10:112681000-112704600	Weak transcription	Right Ventricle	heart
4	chr10:112682000-112700600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:112682000-112702000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:112682000-112702200	Weak transcription	Brain Germinal Matrix	brain
7	chr10:112682000-112704600	Weak transcription	Brain Hippocampus Middle	brain
8	chr10:112682000-112708400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr10:112682000-112732400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:112683000-112700800	Weak transcription	Dnd41	blood
11	chr10:112684200-112700800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr10:112684200-112701000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:112684400-112712600	Weak transcription	HepG2	liver
14	chr10:112685200-112719200	Weak transcription	A549	lung
15	chr10:112687600-112697800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr10:112689400-112704600	Weak transcription	Left Ventricle	heart
17	chr10:112689600-112701600	Weak transcription	Primary B cells from cord blood	blood
18	chr10:112689600-112714400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:112689800-112702200	Weak transcription	Primary T cells from cord blood	blood
20	chr10:112690200-112707800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr10:112690800-112702200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:112691200-112700400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr10:112691800-112703600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr10:112692000-112700800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:112692000-112703200	Weak transcription	Liver	Liver
26	chr10:112692000-112722000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr10:112692400-112700400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr10:112692400-112701200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr10:112692400-112703600	Weak transcription	NHLF	lung
30	chr10:112692400-112704000	Weak transcription	Adipose Nuclei	Adipose
31	chr10:112692400-112704600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr10:112692400-112705400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:112692400-112719000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:112692400-112719000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr10:112692400-112724000	Weak transcription	Stomach Mucosa	stomach
36	chr10:112692600-112699200	Weak transcription	NHDF-Ad	bronchial
37	chr10:112692600-112701800	Weak transcription	HSMM	muscle
38	chr10:112692600-112703200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr10:112692600-112703200	Weak transcription	Osteobl	bone
40	chr10:112692600-112704600	Weak transcription	Psoas Muscle	Psoas
41	chr10:112692600-112705000	Weak transcription	Fetal Heart	heart
42	chr10:112692600-112705000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:112692600-112706400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr10:112692600-112713600	Weak transcription	Hela-S3	cervix
45	chr10:112692600-112732400	Weak transcription	Fetal Intestine Large	intestine
46	chr10:112693000-112702200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr10:112693000-112706800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr10:112693400-112701800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr10:112693400-112702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:112693400-112704600	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links