Variant report

Variant	rs1075379
Chromosome Location	chr6:33737800-33737801
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33736395..33737905-chr6:33740079..33742724,2	K562	blood:
2	chr6:33733421..33736486-chr6:33736727..33739454,3	K562	blood:
3	chr6:33723585..33725981-chr6:33736190..33738429,2	MCF-7	breast:
4	chr6:33734962..33738267-chr6:33754517..33756807,3	K562	blood:
5	chr6:33677151..33680603-chr6:33737180..33740397,3	MCF-7	breast:
6	chr6:33736449..33738043-chr6:34121024..34122876,2	MCF-7	breast:
7	chr6:33725418..33728218-chr6:33736581..33739360,2	MCF-7	breast:
8	chr6:33683560..33685755-chr6:33736435..33739209,2	MCF-7	breast:
9	chr6:33736224..33739190-chr6:33745201..33746852,2	MCF-7	breast:
10	chr6:33734585..33738916-chr6:33755602..33758855,4	MCF-7	breast:
11	chr6:33698259..33701003-chr6:33736395..33738930,2	K562	blood:
12	chr6:33734392..33738843-chr6:33747253..33751824,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161904	Chromatin interaction
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11753083	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11754690	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11755593	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11757524	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11758463	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12524768	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12524835	0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1887340	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes]
rs2281819	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2281820	0.82[CHB][hapmap]
rs2395400	0.90[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2894342	0.85[CEU][hapmap];0.80[GIH][hapmap];0.86[EUR][1000 genomes]
rs3763253	0.85[CEU][hapmap];0.80[GIH][hapmap];0.86[EUR][1000 genomes]
rs3828783	0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4711346	0.91[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55775340	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59137082	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61394483	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61662306	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6904716	0.89[YRI][hapmap]
rs6910736	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6921487	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6930201	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933174	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6933568	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6933607	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6940353	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72880511	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73412140	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73746509	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs747692	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs751096	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs755495	0.90[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7755323	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs943461	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs943462	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs943466	0.90[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.94[EUR][1000 genomes];0.80[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1075379	LEMD2	cis	parietal	SCAN

Chromatin state (count:98 , 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	chr6:33726400-33738200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:33730000-33738600	Weak transcription	A549	lung
4	chr6:33730200-33737800	Weak transcription	Right Atrium	heart
5	chr6:33730200-33738200	Weak transcription	Colonic Mucosa	Colon
6	chr6:33730200-33738400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:33730600-33738600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:33730800-33738600	Weak transcription	Liver	Liver
9	chr6:33731400-33738400	Weak transcription	Spleen	Spleen
10	chr6:33731600-33738200	Weak transcription	Right Ventricle	heart
11	chr6:33732600-33742400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:33734800-33738200	Enhancers	HSMMtube	muscle
13	chr6:33735000-33739600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:33735200-33738200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:33735200-33740000	Enhancers	Fetal Lung	lung
16	chr6:33735400-33739600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr6:33735800-33738800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr6:33736000-33738400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:33736000-33739600	Enhancers	Colon Smooth Muscle	Colon
20	chr6:33736200-33738000	Bivalent Enhancer	Fetal Stomach	stomach
21	chr6:33736200-33738600	Enhancers	HSMM	muscle
22	chr6:33736200-33738800	Enhancers	Stomach Smooth Muscle	stomach
23	chr6:33736200-33739200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:33736200-33739600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:33736200-33740600	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:33736400-33738800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr6:33736400-33739600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:33736400-33739600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:33736400-33739600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:33736400-33740000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:33736600-33737800	Weak transcription	Fetal Brain Female	brain
32	chr6:33736600-33738600	Weak transcription	Thymus	Thymus
33	chr6:33736600-33739000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:33736600-33740000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr6:33736600-33740000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:33736600-33740000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr6:33736600-33740200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:33736600-33740200	Enhancers	HUVEC	blood vessel
39	chr6:33736800-33737800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:33736800-33737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:33736800-33737800	Weak transcription	Fetal Thymus	thymus
42	chr6:33736800-33738000	Weak transcription	Osteobl	bone
43	chr6:33736800-33738200	Weak transcription	Brain Substantia Nigra	brain
44	chr6:33736800-33738400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:33736800-33739600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:33736800-33740000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:33736800-33740000	Weak transcription	GM12878-XiMat	blood
48	chr6:33736800-33740200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:33736800-33741000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:33736800-33743400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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