Variant report

Variant	rs11164939
Chromosome Location	chr1:93953301-93953302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93952150..93954485-chr1:94031536..94034425,2	K562	blood:
2	chr1:93912994..93915026-chr1:93952273..93954304,2	K562	blood:

Variant related genes	Relation type
ENSG00000137942	Chromatin interaction
ENSG00000137936	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11164936	0.81[ASN][1000 genomes]
rs11164941	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12033147	0.81[CEU][hapmap]
rs12034656	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1593516	0.89[ASN][1000 genomes]
rs17109958	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17110058	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs237438	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2391271	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2433279	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2624436	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs3767966	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4847431	0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs61780647	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61784068	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7543847	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs810027	0.81[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11164939	LRRC8D	cis	parietal	SCAN
rs11164939	GBP5	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93937600-93954800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:93943200-93974400	Weak transcription	Fetal Lung	lung
3	chr1:93944000-93974600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:93944200-93954800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:93944200-93971800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:93944200-93974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:93945200-93958000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:93946800-93958000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:93946800-93973200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:93950200-93959400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:93950400-93974800	Weak transcription	HepG2	liver
12	chr1:93950600-93954000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:93951000-93972800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:93951600-93960000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:93951800-93954800	Weak transcription	HUVEC	blood vessel
16	chr1:93952400-93956600	Weak transcription	Small Intestine	intestine
17	chr1:93952400-93958600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:93952600-93953600	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr1:93952600-93954200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:93952600-93973600	Weak transcription	Brain Germinal Matrix	brain
21	chr1:93952800-93959800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:93953200-93953400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:93953200-93953800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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