Variant report

Variant	rs3748043
Chromosome Location	chr5:70751818-70751819
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70751568..70754307-chr5:70852249..70853965,2	K562	blood:
2	chr17:56736055..56736766-chr5:70751336..70751951,2	Hela-S3	cervix:
3	chr5:70742035..70743794-chr5:70750287..70752992,2	MCF-7	breast:
4	chr22:38597715..38598686-chr5:70751398..70751971,2	Hela-S3	cervix:
5	chr5:70749978..70751854-chr5:70881938..70884932,2	K562	blood:
6	chr19:14063240..14063803-chr5:70751277..70752055,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000185022	Chromatin interaction
ENSG00000131844	Chromatin interaction
ENSG00000132017	Chromatin interaction
ENSG00000250387	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10044572	0.89[EUR][1000 genomes]
rs10064079	0.80[TSI][hapmap]
rs10077085	0.89[EUR][1000 genomes]
rs10434642	0.93[EUR][1000 genomes]
rs10462368	0.83[EUR][1000 genomes]
rs10474383	0.93[EUR][1000 genomes]
rs10805884	0.87[EUR][1000 genomes]
rs10942284	0.93[EUR][1000 genomes]
rs10942533	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10942682	0.93[EUR][1000 genomes]
rs10942700	0.87[EUR][1000 genomes]
rs10942702	0.89[EUR][1000 genomes]
rs10942705	0.87[EUR][1000 genomes]
rs11743135	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11746722	0.89[EUR][1000 genomes]
rs12152748	0.88[EUR][1000 genomes]
rs12514732	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516456	0.87[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap]
rs13157835	0.89[EUR][1000 genomes]
rs4062889	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4505929	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5005863	0.91[EUR][1000 genomes]
rs6452722	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6452900	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6453014	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6453018	0.93[EUR][1000 genomes]
rs6453035	0.89[EUR][1000 genomes]
rs6872235	0.89[EUR][1000 genomes]
rs6872671	0.88[EUR][1000 genomes]
rs6877289	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6877773	0.89[EUR][1000 genomes]
rs6886336	0.93[EUR][1000 genomes]
rs6898471	0.91[EUR][1000 genomes]
rs715747	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7378662	0.93[EUR][1000 genomes]
rs7380115	0.89[EUR][1000 genomes]
rs7380280	0.91[EUR][1000 genomes]
rs7444322	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7446049	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7447726	0.93[EUR][1000 genomes]
rs7448422	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7449295	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7714527	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7715648	0.93[EUR][1000 genomes]
rs7721179	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7727576	0.93[EUR][1000 genomes]
rs7728577	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7735544	0.90[EUR][1000 genomes]
rs9968768	0.94[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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
2	nsv528571	chr5:70679626-70767269	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3748043	FAM169A	cis	parietal	SCAN
rs3748043	MCCC2	Cis_1M	lymphoblastoid	RTeQTL
rs3748043	PTCD2	cis	parietal	SCAN
rs3748043	PIK3R1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70750800-70752400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:70750800-70752400	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr5:70750800-70752400	Active TSS	Rectal Smooth Muscle	rectum
4	chr5:70750800-70752600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:70750800-70752600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr5:70750800-70752600	Active TSS	Duodenum Mucosa	Duodenum
7	chr5:70750800-70752800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:70750800-70752800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:70750800-70752800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:70750800-70753000	Active TSS	H1 Cell Line	embryonic stem cell
11	chr5:70750800-70753000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:70750800-70753000	Active TSS	Fetal Kidney	kidney
13	chr5:70750800-70753000	Active TSS	HSMM	muscle
14	chr5:70750800-70753200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:70750800-70753600	Active TSS	A549	lung
16	chr5:70750800-70754400	Active TSS	K562	blood
17	chr5:70751000-70752000	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr5:70751000-70752400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:70751000-70752400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr5:70751000-70752400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:70751000-70752400	Active TSS	Brain Angular Gyrus	brain
22	chr5:70751000-70752400	Active TSS	Brain Anterior Caudate	brain
23	chr5:70751000-70752400	Active TSS	Brain Hippocampus Middle	brain
24	chr5:70751000-70752400	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr5:70751000-70752400	Active TSS	Colonic Mucosa	Colon
26	chr5:70751000-70752400	ZNF genes & repeats	Fetal Brain Male	brain
27	chr5:70751000-70752400	Active TSS	Fetal Heart	heart
28	chr5:70751000-70752400	Active TSS	Fetal Intestine Large	intestine
29	chr5:70751000-70752400	Active TSS	Fetal Thymus	thymus
30	chr5:70751000-70752400	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr5:70751000-70752600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr5:70751000-70752600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr5:70751000-70752600	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr5:70751000-70752600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr5:70751000-70752600	Active TSS	Aorta	Aorta
36	chr5:70751000-70752600	Active TSS	Left Ventricle	heart
37	chr5:70751000-70752800	Active TSS	Fetal Muscle Trunk	muscle
38	chr5:70751000-70752800	Active TSS	Placenta	Placenta
39	chr5:70751000-70752800	Active TSS	Ovary	ovary
40	chr5:70751000-70752800	Active TSS	Thymus	Thymus
41	chr5:70751000-70752800	Active TSS	Hela-S3	cervix
42	chr5:70751000-70752800	Active TSS	NHEK	skin
43	chr5:70751000-70753000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:70751000-70753200	Active TSS	Right Ventricle	heart
45	chr5:70751000-70753200	Active TSS	GM12878-XiMat	blood
46	chr5:70751000-70753400	Active TSS	HMEC	breast
47	chr5:70751000-70753400	Active TSS	NHLF	lung
48	chr5:70751000-70753600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr5:70751000-70753600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:70751200-70752200	Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links