Variant report

Variant	rs4743139
Chromosome Location	chr9:100638420-100638421
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100617184..100619335-chr9:100637041..100639858,3	MCF-7	breast:
2	chr9:100636360..100639098-chr9:100684329..100685877,2	MCF-7	breast:
3	chr9:100637402..100640995-chr9:100649849..100652626,3	MCF-7	breast:
4	chr9:100563307..100565719-chr9:100637927..100639761,2	MCF-7	breast:
5	chr9:100637251..100639094-chr9:100643727..100646653,2	K562	blood:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10046805	0.81[EUR][1000 genomes]
rs10113884	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115216	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10116976	1.00[CHB][hapmap]
rs10117642	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119760	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10119853	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120412	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10122541	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10123699	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124220	1.00[ASN][1000 genomes]
rs10512255	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10739526	0.93[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759975	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759981	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760011	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10760017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10818133	0.81[EUR][1000 genomes]
rs10818175	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818213	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10818241	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10984103	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984230	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10984235	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10984253	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12004762	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12006522	0.93[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12341377	0.81[EUR][1000 genomes]
rs12342417	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12343182	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12347191	0.83[EUR][1000 genomes]
rs12348304	0.81[EUR][1000 genomes]
rs12348691	0.81[EUR][1000 genomes]
rs12550872	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13286291	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13287360	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]
rs13299924	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1348386	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1443432	1.00[ASN][1000 genomes]
rs1443434	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1443435	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1443436	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1561957	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1561961	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1867278	0.81[CEU][hapmap]
rs1955143	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955144	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1955145	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2120264	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2401639	0.81[EUR][1000 genomes]
rs2417575	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2417576	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28703314	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3758248	0.81[EUR][1000 genomes]
rs3758249	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3758251	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs3808893	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3824495	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4255258	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460498	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4743138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4743142	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478413	1.00[ASN][1000 genomes]
rs6478437	0.81[EUR][1000 genomes]
rs6478445	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478469	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6478471	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7022148	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7027221	0.93[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7031386	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032086	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032114	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7034249	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7034336	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7034648	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7036589	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7037175	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7037324	0.93[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7038998	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044121	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044799	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7048255	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851552	0.81[EUR][1000 genomes]
rs7860144	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7866436	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7868534	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs894673	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs907577	0.92[CEU][hapmap]
rs907581	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299258	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9775370	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs993501	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4743139	C9orf156	cis	Frontal Cortex	GTEx
rs4743139	C9orf156	cis	Temporal Cortex	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100631800-100639400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:100635800-100640400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:100636000-100638800	Enhancers	NHEK	skin
4	chr9:100636000-100639200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:100636000-100639200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:100636000-100640400	Enhancers	HMEC	breast
7	chr9:100636400-100638600	Weak transcription	HSMM	muscle
8	chr9:100636600-100638800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:100636600-100639600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:100637600-100658000	Weak transcription	Gastric	stomach
11	chr9:100637800-100639800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:100637800-100652800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:100638000-100642800	Weak transcription	Right Atrium	heart
14	chr9:100638200-100638800	Enhancers	Hela-S3	cervix
15	chr9:100638200-100640000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr9:100638400-100638800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr9:100638400-100639000	Weak transcription	Esophagus	oesophagus
18	chr9:100638400-100639000	Flanking Active TSS	A549	lung
19	chr9:100638400-100639200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:100638400-100640000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr9:100638400-100640200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr9:100638400-100640200	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links