Variant report

Variant	rs265421
Chromosome Location	chr5:114546906-114546907
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	chr5:114546854-114546922	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:114545341..114547918-chr5:114548363..114550045,2	K562	blood:

Variant related genes	Relation type
ENSG00000248175	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs117060	0.84[CHB][hapmap]
rs155414	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155573	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs169088	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs185566	0.88[CHD][hapmap]
rs190561	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2053697	0.92[CHB][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs265412	0.85[CHD][hapmap]
rs265418	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs265419	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs265420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs265424	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs265425	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[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]
rs265430	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs265435	1.00[CEU][hapmap];0.92[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs265436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs265437	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs265438	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs265439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs265442	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs267286	0.88[CHD][hapmap]
rs267295	0.92[CHB][hapmap];0.92[CHD][hapmap]
rs267297	0.89[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs267298	0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs267299	0.84[CHB][hapmap]
rs267300	0.92[CHB][hapmap];0.92[CHD][hapmap]
rs267301	0.84[CHB][hapmap]
rs267302	0.92[CHB][hapmap]
rs267303	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs267304	1.00[ASW][hapmap];0.87[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs267307	0.92[CHB][hapmap];0.92[CHD][hapmap]
rs3100784	0.84[CHB][hapmap];0.92[CHD][hapmap]
rs3111172	0.90[EUR][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	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv970018	chr5:114541040-114547642	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv1029371	chr5:114541428-114590891	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv980715	chr5:114545011-114548142	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs265421	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL
rs265421	CCDC112	cis	parietal	SCAN
rs265421	PGGT1B	cis	lymphoblastoid	seeQTL
rs265421	PGGT1B	cis	multi-tissue	Pritchard

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114523400-114576200	Weak transcription	Psoas Muscle	Psoas
2	chr5:114528000-114563000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:114529200-114562600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:114529800-114551000	Weak transcription	Left Ventricle	heart
5	chr5:114530200-114562600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:114530200-114562600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:114530600-114548600	Weak transcription	Fetal Intestine Large	intestine
8	chr5:114530600-114594400	Weak transcription	Pancreas	Pancrea
9	chr5:114530800-114548000	Weak transcription	Adipose Nuclei	Adipose
10	chr5:114530800-114565200	Weak transcription	NHDF-Ad	bronchial
11	chr5:114531000-114547600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:114531000-114551200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:114531000-114558800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:114531200-114548200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:114532000-114547000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:114533600-114551200	Weak transcription	HSMM	muscle
17	chr5:114533800-114549000	Weak transcription	Aorta	Aorta
18	chr5:114535200-114551200	Weak transcription	HSMMtube	muscle
19	chr5:114536000-114556000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:114538200-114548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:114538200-114551800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:114538400-114548000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:114538400-114548200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:114538400-114567000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:114538400-114572000	Weak transcription	Lung	lung
26	chr5:114538600-114555200	Weak transcription	Placenta	Placenta
27	chr5:114538800-114550800	Weak transcription	Fetal Stomach	stomach
28	chr5:114539200-114580200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:114539400-114547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:114539400-114548000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr5:114539800-114566000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:114540800-114567600	Weak transcription	Hela-S3	cervix
33	chr5:114541000-114562000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:114541200-114548000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:114541400-114548200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:114541600-114551200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:114541800-114548800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:114541800-114549000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:114541800-114573400	Weak transcription	NHLF	lung
40	chr5:114542000-114575800	Weak transcription	Small Intestine	intestine
41	chr5:114542600-114549000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:114543200-114548800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:114543400-114548600	Weak transcription	Ovary	ovary
44	chr5:114543400-114549800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:114543600-114548000	Weak transcription	Fetal Muscle Leg	muscle
46	chr5:114543600-114551200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:114543600-114551200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:114543600-114558800	Weak transcription	NH-A	brain
49	chr5:114543600-114562400	Weak transcription	HUVEC	blood vessel
50	chr5:114543800-114562800	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links