Variant report

Variant	rs6540844
Chromosome Location	chr1:214680378-214680379
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:214677645..214681280-chr1:214723322..214726744,5	MCF-7	breast:
2	chr1:214678638..214681169-chr1:214682598..214685287,2	MCF-7	breast:
3	chr1:214679463..214680976-chr1:214683287..214685488,2	K562	blood:

Variant related genes	Relation type
ENSG00000152104	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12073252	0.83[CHB][hapmap]
rs17042140	0.90[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34952927	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs4414018	0.83[CHB][hapmap]
rs6665967	0.85[CHB][hapmap]
rs6693492	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs7531731	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv468094	chr1:214654965-214687725	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv549180	chr1:214654965-214687725	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6540844	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:214665400-214705400	Weak transcription	Right Ventricle	heart
2	chr1:214668400-214680400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:214669800-214700400	Weak transcription	Aorta	Aorta
4	chr1:214671800-214686800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:214674200-214685200	Weak transcription	HUVEC	blood vessel
6	chr1:214674200-214687200	Weak transcription	HSMMtube	muscle
7	chr1:214674400-214685000	Weak transcription	Fetal Stomach	stomach
8	chr1:214674600-214686800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:214676600-214681000	Enhancers	Stomach Mucosa	stomach
10	chr1:214676800-214681400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:214677000-214681600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:214677200-214690200	Weak transcription	Small Intestine	intestine
13	chr1:214677600-214680800	Enhancers	Pancreas	Pancrea
14	chr1:214678000-214686800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:214678200-214680400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:214678200-214683400	Weak transcription	Gastric	stomach
17	chr1:214678200-214685400	Weak transcription	Esophagus	oesophagus
18	chr1:214678200-214687800	Weak transcription	Lung	lung
19	chr1:214678400-214681600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:214678600-214680800	Enhancers	Duodenum Mucosa	Duodenum
21	chr1:214678600-214680800	Enhancers	Placenta	Placenta
22	chr1:214679000-214680600	Weak transcription	Right Atrium	heart
23	chr1:214679000-214684000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:214679000-214687400	Weak transcription	Ovary	ovary
25	chr1:214679200-214680800	Weak transcription	NHLF	lung
26	chr1:214679200-214681200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:214679200-214687800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:214679400-214680600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr1:214679400-214681200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:214679400-214681200	Enhancers	Fetal Intestine Small	intestine
31	chr1:214679400-214681200	Enhancers	HMEC	breast
32	chr1:214679400-214683400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:214679600-214681400	Enhancers	Dnd41	blood
34	chr1:214679600-214687600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:214679800-214681000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:214679800-214682600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:214680000-214680400	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr1:214680000-214680400	Flanking Active TSS	HepG2	liver
39	chr1:214680000-214680400	Genic enhancers	HSMM	muscle
40	chr1:214680000-214680600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:214680000-214680800	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:214680000-214680800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:214680000-214680800	Enhancers	Psoas Muscle	Psoas
44	chr1:214680000-214680800	Enhancers	Rectal Smooth Muscle	rectum
45	chr1:214680000-214680800	Enhancers	NHDF-Ad	bronchial
46	chr1:214680000-214680800	Flanking Active TSS	NHEK	skin
47	chr1:214680000-214681000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr1:214680000-214681000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:214680000-214681000	Enhancers	NH-A	brain
50	chr1:214680000-214681200	Enhancers	HUES64 Cell Line	embryonic stem cell

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