Variant report

Variant	rs41408448
Chromosome Location	chr5:1642155-1642156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1474066..1474782-chr5:1641613..1642314,2	MCF-7	breast:
2	chr5:1479600..1480449-chr5:1641359..1642320,8	K562	blood:
3	chr5:1601351..1602385-chr5:1641606..1642321,3	MCF-7	breast:
4	chr5:1594724..1595423-chr5:1641483..1642314,2	K562	blood:
5	chr5:1168197..1168876-chr5:1641446..1642294,3	MCF-7	breast:
6	chr5:1637235..1639210-chr5:1639365..1642347,2	K562	blood:
7	chr5:1209132..1210132-chr5:1641419..1642353,2	K562	blood:

Variant related genes	Relation type
ENSG00000185986	Chromatin interaction
ENSG00000271119	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10040389	0.94[ASN][1000 genomes]
rs10052477	0.95[CEU][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10061756	0.88[ASN][1000 genomes]
rs10062809	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10062957	0.94[ASN][1000 genomes]
rs10074018	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10474721	0.94[ASN][1000 genomes]
rs10475075	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10475076	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10475077	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12153695	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55854954	0.90[ASN][1000 genomes]
rs58775025	0.87[ASN][1000 genomes]
rs6554915	0.86[ASW][hapmap];0.80[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs72719219	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719222	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7705049	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7734561	0.83[GIH][hapmap];0.89[JPT][hapmap]
rs9312909	0.89[JPT][hapmap];0.90[ASN][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	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking 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	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv881328	chr5:1637461-1671200	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs41408448	CTD-2012J19.1	cis	lung	GTEx
rs41408448	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs41408448	RP11-43F13.1	cis	Adipose Subcutaneous	GTEx
rs41408448	CTD-2012J19.1	cis	Thyroid	GTEx
rs41408448	RP11-43F13.1	cis	Muscle Skeletal	GTEx
rs41408448	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs41408448	PLEKHG4B	cis	cerebellum	SCAN
rs41408448	KIAA0947	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
2	chr5:1634600-1645200	Weak transcription	Gastric	stomach
3	chr5:1640000-1642400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:1640000-1642800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr5:1640400-1642400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:1640400-1643000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:1641200-1642200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:1641400-1642200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:1641400-1642200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr5:1641400-1642200	Enhancers	Fetal Heart	heart
11	chr5:1641400-1643000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:1641600-1642200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr5:1641600-1642200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr5:1641600-1642200	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr5:1641600-1642200	Enhancers	Fetal Brain Male	brain
16	chr5:1641600-1642400	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr5:1641600-1642400	Enhancers	Hela-S3	cervix
18	chr5:1641600-1643000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr5:1641800-1642200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr5:1641800-1642200	Bivalent Enhancer	NH-A	brain
21	chr5:1642000-1642200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
22	chr5:1642000-1642200	Enhancers	Liver	Liver
23	chr5:1642000-1642200	Enhancers	A549	lung
24	chr5:1642000-1642400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links