Variant report

Variant	rs2067997
Chromosome Location	chr6:35471246-35471247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1883636	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3777746	1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs3798344	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45493300	0.80[EUR][1000 genomes]
rs56313753	0.86[ASN][1000 genomes]
rs6928735	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929353	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7738975	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7768844	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9689798	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
2	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases
3	nsv462909	chr6:35457396-35502202	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv602912	chr6:35457396-35502202	Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
5	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1820663	chr6:35464197-35471362	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	esv2761067	chr6:35471246-35573245	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2067997	LEMD2	cis	cerebellum	SCAN
rs2067997	SRPK1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35466400-35476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr6:35466400-35479200	Weak transcription	Right Ventricle	heart
3	chr6:35466800-35477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:35466800-35479400	Weak transcription	Right Atrium	heart
5	chr6:35467000-35473400	Weak transcription	Esophagus	oesophagus
6	chr6:35467400-35478600	Weak transcription	Fetal Lung	lung
7	chr6:35467600-35471600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:35468800-35473000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:35469000-35473200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:35469000-35473600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:35469200-35471400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:35469200-35473400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:35469200-35473600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:35469200-35473600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:35469200-35473600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:35469200-35473800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:35469200-35474200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:35469800-35471800	Enhancers	Placenta	Placenta
19	chr6:35469800-35473200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:35470400-35472200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr6:35470600-35471400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:35471000-35472000	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:35471200-35471400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr6:35471200-35471400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr6:35471200-35471400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr6:35471200-35471600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr6:35471200-35471600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
28	chr6:35471200-35471600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:35471200-35471600	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr6:35471200-35471600	Bivalent Enhancer	Fetal Thymus	thymus
31	chr6:35471200-35471600	Enhancers	Psoas Muscle	Psoas
32	chr6:35471200-35471800	Enhancers	HSMMtube	muscle
33	chr6:35471200-35472000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:35471200-35472000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:35471200-35472400	Bivalent Enhancer	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links