Variant report

Variant	rs9383940
Chromosome Location	chr6:150226059-150226060
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150157068..150159142-chr6:150224629..150226824,2	MCF-7	breast:
2	chr6:150225385..150227618-chr6:150231399..150233931,2	MCF-7	breast:
3	chr6:150182462..150186110-chr6:150225717..150228741,3	MCF-7	breast:
4	chr6:150222304..150224162-chr6:150225800..150228066,2	MCF-7	breast:
5	chr6:150195717..150198563-chr6:150225615..150228061,2	K562	blood:

Variant related genes	Relation type
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1334510	1.00[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17748069	0.83[CHD][hapmap];0.87[MEX][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2095376	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2342767	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2342768	0.84[EUR][1000 genomes]
rs2342769	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2342770	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3823021	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4242281	0.93[CHB][hapmap];0.95[ASN][1000 genomes]
rs4458704	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[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869763	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4869764	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4870109	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4870116	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6557133	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6933882	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6935829	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6939761	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7740145	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7742692	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7742993	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7744821	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7747435	0.92[EUR][1000 genomes]
rs7747457	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7753544	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7756850	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs7757972	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7757984	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7758020	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7758033	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7763719	0.87[AMR][1000 genomes]
rs7763849	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7764376	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7767588	0.94[EUR][1000 genomes]
rs7767592	0.94[EUR][1000 genomes]
rs7768626	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7768665	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7769118	1.00[CEU][hapmap];0.81[JPT][hapmap];0.94[EUR][1000 genomes]
rs7771014	0.90[EUR][1000 genomes]
rs7774787	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9322225	0.83[EUR][1000 genomes]
rs9322228	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9371215	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9371223	1.00[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9371504	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9371505	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9371533	0.92[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9371542	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs9371544	0.88[CEU][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9383577	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9383584	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9383912	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9383913	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9383914	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9383921	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9397058	1.00[CEU][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9397398	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9397420	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9397434	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9397438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9478241	0.96[ASN][1000 genomes]
rs9968871	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9969044	1.00[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs9986576	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs9383940	LRP11	cis	cerebellum	SCAN
rs9383940	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9383940	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9383940	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9383940	LRP11	cis	Adipose Subcutaneous	GTEx
rs9383940	PPIL4	cis	cerebellum	SCAN
rs9383940	RP11-350J20.9	cis	Heart Left Ventricle	GTEx
rs9383940	RP11-350J20.9	cis	Muscle Skeletal	GTEx
rs9383940	LATS1	cis	parietal	SCAN
rs9383940	RP11-350J20.5	cis	Thyroid	GTEx
rs9383940	AKAP12	cis	cerebellum	SCAN
rs9383940	DKK2	trans	cerebellum	SCAN
rs9383940	RAET1E	cis	Nerve Tibial	GTEx
rs9383940	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9383940	RP11-350J20.5	cis	lung	GTEx
rs9383940	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9383940	RP11-350J20.9	cis	lung	GTEx
rs9383940	RAET1G	cis	Artery Tibial	GTEx
rs9383940	LRP11	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150218800-150227600	Weak transcription	Fetal Intestine Small	intestine
2	chr6:150219200-150226200	Weak transcription	Spleen	Spleen
3	chr6:150222600-150226600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:150222600-150229800	Weak transcription	Pancreas	Pancrea
5	chr6:150223000-150226600	Weak transcription	Esophagus	oesophagus
6	chr6:150225200-150227400	Enhancers	Fetal Muscle Leg	muscle
7	chr6:150225400-150226200	Enhancers	Stomach Smooth Muscle	stomach
8	chr6:150225400-150227200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr6:150225400-150227600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr6:150225400-150227800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:150225600-150226400	Weak transcription	Right Ventricle	heart
12	chr6:150225800-150226200	Enhancers	Right Atrium	heart
13	chr6:150226000-150227800	Enhancers	Lung	lung

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