Variant report

Variant	rs10787291
Chromosome Location	chr10:112664781-112664782
allele	G/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	chr10:112660041-112665005	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:112629865..112631826-chr10:112663124..112665657,2	K562	blood:
2	chr10:112664345..112669629-chr10:112675236..112680543,10	K562	blood:
3	chr10:112664593..112668677-chr10:112669632..112672354,5	MCF-7	breast:

Variant related genes	Relation type
BBIP1	TF binding region
ENSG00000214413	Chromatin interaction
ENSG00000108061	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000270589	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10082499	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10787286	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10787293	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10787299	0.87[EUR][1000 genomes]
rs10885059	0.82[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885060	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10885064	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10885071	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10885076	0.90[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs11195381	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11195387	0.90[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11195390	0.90[CEU][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11195391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11195398	0.90[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12240685	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12242177	0.87[EUR][1000 genomes]
rs12242928	0.87[EUR][1000 genomes]
rs12246561	0.87[ASW][hapmap]
rs12261765	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12776359	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12776861	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12783690	1.00[JPT][hapmap]
rs2146544	0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs34401279	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34893229	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35394459	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35793075	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35946882	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3750619	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763692	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4917589	1.00[JPT][hapmap]
rs6585026	0.90[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7089687	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7096359	0.87[ASW][hapmap]
rs7919142	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9663346	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10787291	HABP2	cis	parietal	SCAN
rs10787291	XPNPEP1	cis	cerebellum	SCAN
rs10787291	LOC92482	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112632800-112678000	Weak transcription	Lung	lung
2	chr10:112632800-112678200	Weak transcription	Spleen	Spleen
3	chr10:112634800-112677400	Weak transcription	HUVEC	blood vessel
4	chr10:112636400-112664800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:112643000-112667200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr10:112644200-112678000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:112644800-112664800	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr10:112644800-112675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr10:112646400-112676400	Weak transcription	K562	blood
10	chr10:112647200-112677400	Weak transcription	Fetal Brain Male	brain
11	chr10:112649400-112664800	Strong transcription	Primary B cells from cord blood	blood
12	chr10:112651200-112670000	Weak transcription	Fetal Stomach	stomach
13	chr10:112654800-112665000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr10:112656200-112672200	Weak transcription	Fetal Heart	heart
15	chr10:112656200-112677400	Weak transcription	Stomach Mucosa	stomach
16	chr10:112656400-112676400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:112656400-112677600	Weak transcription	Right Ventricle	heart
18	chr10:112657200-112672400	Weak transcription	Fetal Intestine Small	intestine
19	chr10:112657200-112675000	Weak transcription	Ovary	ovary
20	chr10:112657400-112665200	Weak transcription	Esophagus	oesophagus
21	chr10:112657400-112672800	Weak transcription	HepG2	liver
22	chr10:112657400-112677600	Weak transcription	Psoas Muscle	Psoas
23	chr10:112657400-112677600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:112657400-112677800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr10:112657400-112677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:112657400-112678000	Weak transcription	Gastric	stomach
27	chr10:112657600-112677600	Weak transcription	Fetal Brain Female	brain
28	chr10:112659200-112667000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr10:112659200-112676400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr10:112659400-112677600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr10:112659600-112677600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr10:112659800-112675800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr10:112660200-112676000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr10:112660400-112670200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr10:112660400-112675800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr10:112660400-112676200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:112660400-112677000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr10:112660600-112677200	Weak transcription	Dnd41	blood
39	chr10:112661000-112667000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr10:112661000-112677000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr10:112661000-112677200	Weak transcription	Fetal Intestine Large	intestine
42	chr10:112661200-112676400	Weak transcription	Aorta	Aorta
43	chr10:112661400-112666600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:112661400-112671000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr10:112661600-112677600	Weak transcription	Brain Germinal Matrix	brain
46	chr10:112661800-112666200	Weak transcription	Pancreas	Pancrea
47	chr10:112661800-112675000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr10:112661800-112676000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr10:112662000-112676000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:112662200-112665400	Weak transcription	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links