Variant report

Variant	rs11737346
Chromosome Location	chr4:148763687-148763688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148671335..148673992-chr4:148761092..148763924,2	MCF-7	breast:
2	chr4:148652686..148654592-chr4:148763097..148764811,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071205	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10007231	0.92[CEU][hapmap]
rs10014696	0.84[JPT][hapmap]
rs10023057	0.92[CEU][hapmap]
rs10026985	0.85[JPT][hapmap]
rs1013842	0.92[CEU][hapmap]
rs10461235	0.92[CEU][hapmap]
rs11733409	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12498257	0.92[CEU][hapmap]
rs13129325	0.85[JPT][hapmap]
rs13148956	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1436489	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1436490	0.85[EUR][1000 genomes]
rs1469865	0.92[CEU][hapmap]
rs1469867	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17613979	0.84[JPT][hapmap]
rs17614025	0.93[MKK][hapmap]
rs28662484	0.85[EUR][1000 genomes]
rs35810358	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4240341	0.84[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4835101	0.80[EUR][1000 genomes]
rs4835103	0.90[JPT][hapmap]
rs4835461	0.92[CEU][hapmap]
rs4835463	0.92[CEU][hapmap]
rs4835469	0.80[MKK][hapmap]
rs6832527	0.83[ASN][1000 genomes]
rs6846526	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6846899	0.92[CEU][hapmap];0.80[CHB][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7654433	0.92[CEU][hapmap]
rs7656471	0.84[ASN][1000 genomes]
rs7698670	0.91[ASN][1000 genomes]
rs893024	0.92[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs9991741	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9995956	0.85[JPT][hapmap]
rs9997027	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11737346	LSM6	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148737800-148782200	Weak transcription	Thymus	Thymus
2	chr4:148743200-148782200	Weak transcription	Fetal Intestine Large	intestine
3	chr4:148746400-148768000	Weak transcription	Fetal Intestine Small	intestine
4	chr4:148751400-148776000	Weak transcription	Fetal Stomach	stomach
5	chr4:148753200-148765800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:148753200-148767800	Weak transcription	Small Intestine	intestine
7	chr4:148753400-148765800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:148753400-148782000	Weak transcription	Gastric	stomach
9	chr4:148754000-148766200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:148754400-148769000	Weak transcription	NHLF	lung
11	chr4:148754600-148764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:148755600-148773200	Weak transcription	Esophagus	oesophagus
13	chr4:148755800-148764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:148756400-148766000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:148756400-148768000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:148756800-148766200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:148756800-148777800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr4:148757400-148767400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:148757400-148767600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:148757600-148766200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr4:148757800-148763800	Weak transcription	HSMMtube	muscle
22	chr4:148760800-148764600	Enhancers	Colon Smooth Muscle	Colon
23	chr4:148761000-148764600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr4:148761000-148764600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:148761200-148764200	Enhancers	Adipose Nuclei	Adipose
26	chr4:148761200-148764400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:148761200-148764800	Enhancers	Fetal Muscle Leg	muscle
28	chr4:148761400-148764200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:148761400-148767800	Weak transcription	Fetal Kidney	kidney
30	chr4:148761800-148763800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr4:148761800-148764600	Enhancers	Psoas Muscle	Psoas
32	chr4:148761800-148765200	Enhancers	Right Atrium	heart
33	chr4:148762000-148764200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:148762200-148764200	Enhancers	Stomach Smooth Muscle	stomach
35	chr4:148762200-148767400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:148762400-148763800	Weak transcription	Brain Angular Gyrus	brain
37	chr4:148762400-148763800	Weak transcription	Lung	lung
38	chr4:148762400-148763800	Weak transcription	Right Ventricle	heart
39	chr4:148762400-148767000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:148762400-148770000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr4:148762400-148771000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:148762600-148767600	Weak transcription	Fetal Lung	lung
43	chr4:148762800-148775400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:148763000-148764600	Enhancers	Rectal Smooth Muscle	rectum
45	chr4:148763000-148765000	Enhancers	Fetal Muscle Trunk	muscle
46	chr4:148763000-148765200	Enhancers	Left Ventricle	heart
47	chr4:148763000-148765200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr4:148763200-148763800	Weak transcription	Ovary	ovary
49	chr4:148763200-148764400	Weak transcription	GM12878-XiMat	blood
50	chr4:148763200-148764600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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