Variant report

Variant	rs4711347
Chromosome Location	chr6:33735292-33735293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33728564..33732066-chr6:33733725..33737558,5	MCF-7	breast:
2	chr6:33712629..33714583-chr6:33734231..33736589,2	MCF-7	breast:
3	chr6:33734321..33736255-chr6:34120616..34122226,2	MCF-7	breast:
4	chr6:33733922..33735455-chr6:33738926..33740913,2	MCF-7	breast:
5	chr6:33733658..33736198-chr6:33737954..33739952,2	K562	blood:
6	chr6:33734962..33738267-chr6:33754517..33756807,3	K562	blood:
7	chr6:33732354..33734796-chr6:33734914..33737120,3	K562	blood:
8	chr6:33717632..33719728-chr6:33734198..33737184,2	K562	blood:
9	chr6:33683155..33686367-chr6:33732476..33736646,4	MCF-7	breast:
10	chr6:33727358..33730164-chr6:33732846..33736236,4	K562	blood:
11	chr6:33715170..33717899-chr6:33734548..33736786,2	MCF-7	breast:
12	chr6:33733421..33736486-chr6:33736727..33739454,3	K562	blood:
13	chr6:33678384..33680864-chr6:33733312..33735664,3	MCF-7	breast:
14	chr6:33734585..33738916-chr6:33755602..33758855,4	MCF-7	breast:
15	chr6:33733565..33735382-chr6:33741109..33742921,2	K562	blood:
16	chr6:33587894..33590790-chr6:33732523..33735377,2	MCF-7	breast:
17	chr6:33734392..33738843-chr6:33747253..33751824,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction
ENSG00000137288	Chromatin interaction
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11752297	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12173787	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281820	0.83[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs2296743	0.81[CHD][hapmap]
rs2296744	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2395402	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3806109	0.81[CHD][hapmap]
rs4342423	0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs4711348	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711349	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4711355	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713678	0.82[EUR][1000 genomes]
rs4713679	0.83[EUR][1000 genomes]
rs6457741	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6904991	0.82[YRI][hapmap]
rs6920075	0.82[AFR][1000 genomes]
rs6922275	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6929696	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs747694	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs755496	0.81[CHD][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs7774620	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357164	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9394165	0.82[YRI][hapmap]
rs9394167	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs943471	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs943474	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs943475	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs943478	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs943479	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv462897	chr6:33717770-33778964	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv602839	chr6:33717770-33778964	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv462898	chr6:33723383-33768897	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv602840	chr6:33723383-33768897	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4711347	PSMB9	cis	lymphoblastoid	seeQTL
rs4711347	LEMD2	cis	cerebellum	SCAN
rs4711347	LEMD2	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33715200-33737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:33723400-33736600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:33729000-33736200	Weak transcription	HSMM	muscle
5	chr6:33730000-33738600	Weak transcription	A549	lung
6	chr6:33730200-33736400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr6:33730200-33737800	Weak transcription	Right Atrium	heart
8	chr6:33730200-33738200	Weak transcription	Colonic Mucosa	Colon
9	chr6:33730200-33738400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:33730600-33738600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr6:33730800-33736000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:33730800-33736600	Weak transcription	Brain Substantia Nigra	brain
13	chr6:33730800-33737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:33730800-33738600	Weak transcription	Liver	Liver
15	chr6:33731400-33738400	Weak transcription	Spleen	Spleen
16	chr6:33731600-33738200	Weak transcription	Right Ventricle	heart
17	chr6:33731800-33735400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:33732000-33736200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:33733800-33736400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:33734800-33738200	Enhancers	HSMMtube	muscle
22	chr6:33735000-33735600	Enhancers	Adipose Nuclei	Adipose
23	chr6:33735000-33739600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:33735200-33736200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:33735200-33736400	Enhancers	Fetal Muscle Trunk	muscle
26	chr6:33735200-33738200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:33735200-33740000	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links