Variant report

Variant	rs2281820
Chromosome Location	chr6:33768897-33768898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33758412..33760501-chr6:33767524..33770306,2	MCF-7	breast:
2	chr6:33767158..33770119-chr6:33775833..33777551,2	MCF-7	breast:
3	chr6:33762823..33764594-chr6:33767158..33770034,2	K562	blood:
4	chr6:33767719..33770571-chr6:33780655..33782252,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1075379	0.82[CHB][hapmap]
rs11754690	0.90[CHB][hapmap]
rs12173787	0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs12524835	0.90[CHB][hapmap]
rs1887340	0.90[CHB][hapmap]
rs2296744	0.92[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2395402	0.80[CHD][hapmap];0.92[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs3828783	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs4711346	0.91[CHB][hapmap]
rs4711347	0.83[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs4711348	0.92[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs4711349	0.89[EUR][1000 genomes]
rs4711355	0.90[EUR][1000 genomes]
rs4713678	0.87[EUR][1000 genomes]
rs6457741	0.90[EUR][1000 genomes]
rs6922275	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6929696	0.80[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs6933607	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs747692	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs747694	0.84[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs751096	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs755495	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs7755323	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs7774620	0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs9357164	0.90[EUR][1000 genomes]
rs9366829	0.88[ASW][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9394167	0.80[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs943462	0.91[CHB][hapmap]
rs943466	0.82[CHB][hapmap]
rs943471	0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs943474	0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs943475	0.80[CHD][hapmap];0.92[JPT][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs943478	0.89[EUR][1000 genomes]
rs943479	0.92[JPT][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2281820	LEMD2	cis	cerebellum	SCAN
rs2281820	LEMD2	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33757600-33775800	Weak transcription	Right Atrium	heart
2	chr6:33763600-33771600	Weak transcription	Fetal Intestine Small	intestine
3	chr6:33765800-33769200	Weak transcription	Brain Germinal Matrix	brain
4	chr6:33765800-33770200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:33766000-33769200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:33766000-33770200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:33766000-33776000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:33766200-33769000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:33766600-33770000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:33766800-33769800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:33766800-33776400	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:33767800-33769000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:33768200-33770000	Weak transcription	Osteobl	bone
14	chr6:33768400-33770600	Weak transcription	NHDF-Ad	bronchial
15	chr6:33768600-33769400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:33768600-33769600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
17	chr6:33768800-33769000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:33768800-33769000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:33768800-33769000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:33768800-33772400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links