Variant report

Variant	rs747694
Chromosome Location	chr6:33736490-33736491
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33728564..33732066-chr6:33733725..33737558,5	MCF-7	breast:
2	chr6:33736395..33737905-chr6:33740079..33742724,2	K562	blood:
3	chr6:33712629..33714583-chr6:33734231..33736589,2	MCF-7	breast:
4	chr6:33736439..33736983-chr6:34022692..34023404,3	K562	blood:
5	chr6:33723585..33725981-chr6:33736190..33738429,2	MCF-7	breast:
6	chr6:33735900..33737654-chr6:33755240..33757929,2	MCF-7	breast:
7	chr6:33734962..33738267-chr6:33754517..33756807,3	K562	blood:
8	chr6:33736449..33738043-chr6:34121024..34122876,2	MCF-7	breast:
9	chr6:33736023..33736621-chr6:33995139..33996006,3	K562	blood:
10	chr6:33732354..33734796-chr6:33734914..33737120,3	K562	blood:
11	chr6:33717632..33719728-chr6:33734198..33737184,2	K562	blood:
12	chr6:33683155..33686367-chr6:33732476..33736646,4	MCF-7	breast:
13	chr6:33715170..33717899-chr6:33734548..33736786,2	MCF-7	breast:
14	chr6:33683560..33685755-chr6:33736435..33739209,2	MCF-7	breast:
15	chr6:33736224..33739190-chr6:33745201..33746852,2	MCF-7	breast:
16	chr6:33734585..33738916-chr6:33755602..33758855,4	MCF-7	breast:
17	chr6:33698259..33701003-chr6:33736395..33738930,2	K562	blood:
18	chr6:33734392..33738843-chr6:33747253..33751824,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12173787	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12190029	0.80[AMR][1000 genomes]
rs2281820	0.84[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs2296744	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2395402	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4711347	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]
rs4711348	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711349	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4711355	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713678	0.84[EUR][1000 genomes]
rs4713679	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6457741	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922275	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6929696	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747695	0.83[AFR][1000 genomes]
rs7774620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357164	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394167	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs943474	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943475	0.96[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943478	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs943479	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[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
rs747694	PSMB9	cis	lymphoblastoid	seeQTL
rs747694	LEMD2	cis	cerebellum	SCAN
rs747694	LEMD2	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr6:33730000-33738600	Weak transcription	A549	lung
5	chr6:33730200-33737800	Weak transcription	Right Atrium	heart
6	chr6:33730200-33738200	Weak transcription	Colonic Mucosa	Colon
7	chr6:33730200-33738400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:33730600-33738600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:33730800-33736600	Weak transcription	Brain Substantia Nigra	brain
10	chr6:33730800-33737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:33730800-33738600	Weak transcription	Liver	Liver
12	chr6:33731400-33738400	Weak transcription	Spleen	Spleen
13	chr6:33731600-33738200	Weak transcription	Right Ventricle	heart
14	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:33734800-33738200	Enhancers	HSMMtube	muscle
16	chr6:33735000-33739600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:33735200-33738200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:33735200-33740000	Enhancers	Fetal Lung	lung
19	chr6:33735400-33739600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr6:33735600-33736600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:33735600-33737000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:33735800-33737000	Enhancers	NHLF	lung
23	chr6:33735800-33738800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:33736000-33738400	Enhancers	Muscle Satellite Cultured Cells	--
25	chr6:33736000-33739600	Enhancers	Colon Smooth Muscle	Colon
26	chr6:33736200-33736600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:33736200-33736800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr6:33736200-33736800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr6:33736200-33736800	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:33736200-33736800	Enhancers	Brain Hippocampus Middle	brain
31	chr6:33736200-33736800	Bivalent Enhancer	Placenta	Placenta
32	chr6:33736200-33738000	Bivalent Enhancer	Fetal Stomach	stomach
33	chr6:33736200-33738600	Enhancers	HSMM	muscle
34	chr6:33736200-33738800	Enhancers	Stomach Smooth Muscle	stomach
35	chr6:33736200-33739200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:33736200-33739600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:33736200-33740600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr6:33736400-33736600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:33736400-33736600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:33736400-33736600	Enhancers	Thymus	Thymus
41	chr6:33736400-33736800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr6:33736400-33736800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:33736400-33736800	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr6:33736400-33736800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr6:33736400-33736800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:33736400-33737200	Enhancers	Fetal Muscle Leg	muscle
47	chr6:33736400-33738800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr6:33736400-33739600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:33736400-33739600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:33736400-33739600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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