Variant report

Variant	rs9394169
Chromosome Location	chr6:33778964-33778965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10947439	0.93[JPT][hapmap]
rs1547669	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1547670	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7774407	0.86[CHD][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap]
rs9380379	0.80[YRI][hapmap]

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	nsv885773	chr6:33778964-33813043	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv885774	chr6:33778964-33840121	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9394169	LEMD2	cis	parietal	SCAN
rs9394169	ITPR3	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33776400-33792400	Weak transcription	Right Atrium	heart
2	chr6:33778400-33779000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:33778400-33779400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:33778400-33779800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr6:33778400-33779800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr6:33778400-33780200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:33778400-33781000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:33778400-33782400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:33778600-33779000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:33778600-33780600	Enhancers	H9 Cell Line	embryonic stem cell
11	chr6:33778600-33781800	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:33778600-33784000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:33778800-33779200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:33778800-33779400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:33778800-33780600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:33778800-33781800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:33778800-33782200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:33778800-33782200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:33778800-33782800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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