Variant report

Variant	rs10776775
Chromosome Location	chr1:114436482-114436483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114434553..114437151-chr1:114470890..114472929,2	K562	blood:
2	chr1:114417906..114420931-chr1:114435786..114438695,3	MCF-7	breast:
3	chr1:114300443..114302096-chr1:114435414..114436958,2	K562	blood:
4	chr1:114422800..114426038-chr1:114435058..114437356,3	MCF-7	breast:
5	chr1:114354283..114356769-chr1:114434913..114437016,3	MCF-7	breast:
6	chr1:114435789..114438418-chr1:114440934..114442549,2	MCF-7	breast:
7	chr1:114429070..114435293-chr1:114435414..114441720,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235527	Chromatin interaction
ENSG00000188761	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000081019	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10745340	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];0.94[MKK][hapmap];1.00[TSI][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]
rs10858022	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10858023	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11102701	0.81[AFR][1000 genomes]
rs11582409	0.85[YRI][hapmap]
rs11584821	0.85[YRI][hapmap]
rs1217382	0.87[YRI][hapmap]
rs1217391	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1217392	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217394	0.84[CHD][hapmap]
rs1539438	0.84[CHD][hapmap]
rs17464525	1.00[YRI][hapmap]
rs17510162	0.85[YRI][hapmap]
rs2358994	0.80[MEX][hapmap]
rs3765598	0.85[YRI][hapmap]
rs3789613	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];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3811021	0.85[YRI][hapmap]
rs3827733	0.85[YRI][hapmap]
rs6661817	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700802	0.85[YRI][hapmap]
rs7523862	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524200	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]

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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10776775	PHTF1	cis	cerebellum	SCAN
rs10776775	AP4B1	cis	multi-tissue	Pritchard
rs10776775	CTTNBP2NL	cis	parietal	SCAN
rs10776775	FILIP1L	trans	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114415000-114447000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:114415400-114437000	Weak transcription	Thymus	Thymus
3	chr1:114417200-114437000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:114420200-114437800	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:114420200-114446400	Weak transcription	Aorta	Aorta
6	chr1:114424200-114437800	Weak transcription	Brain Germinal Matrix	brain
7	chr1:114424600-114436600	Weak transcription	Fetal Thymus	thymus
8	chr1:114424600-114437800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:114424600-114438800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:114424600-114442400	Weak transcription	Psoas Muscle	Psoas
11	chr1:114425000-114436800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:114425400-114437400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:114427200-114436800	Weak transcription	Fetal Brain Female	brain
14	chr1:114427400-114437000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:114427600-114437800	Weak transcription	Brain Angular Gyrus	brain
16	chr1:114428200-114437000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:114428200-114437800	Weak transcription	Lung	lung
18	chr1:114428600-114437800	Weak transcription	Esophagus	oesophagus
19	chr1:114429200-114437600	Weak transcription	HSMMtube	muscle
20	chr1:114430000-114437400	Weak transcription	Placenta	Placenta
21	chr1:114430000-114437800	Weak transcription	Colonic Mucosa	Colon
22	chr1:114430000-114437800	Weak transcription	Left Ventricle	heart
23	chr1:114430000-114437800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:114430000-114440000	Weak transcription	Pancreas	Pancrea
25	chr1:114430000-114442400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:114430200-114438400	Weak transcription	Fetal Stomach	stomach
27	chr1:114430400-114436600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:114430400-114437400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:114430400-114440000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:114430600-114436800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:114430600-114436800	Weak transcription	Dnd41	blood
32	chr1:114430600-114437200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:114430600-114437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:114430600-114437200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:114430600-114437600	Weak transcription	K562	blood
36	chr1:114430800-114436600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:114430800-114436800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:114430800-114437200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:114430800-114437200	Weak transcription	Hela-S3	cervix
40	chr1:114430800-114437400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:114430800-114437400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:114430800-114437600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:114430800-114437800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:114430800-114437800	Weak transcription	NHEK	skin
45	chr1:114430800-114440200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:114431000-114437000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:114431000-114438800	Weak transcription	A549	lung
48	chr1:114431800-114437200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:114431800-114437200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:114431800-114445400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links