Variant report

Variant	rs11922973
Chromosome Location	chr3:118700611-118700612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1016284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709001	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11709968	1.00[ASW][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715148	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12053925	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1435653	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17738897	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1836689	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1836691	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1879553	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2160050	0.94[ASN][1000 genomes]
rs4405907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687832	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687834	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687836	0.82[TSI][hapmap]
rs4687960	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55742142	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56232409	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56234333	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs60755482	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7636874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2756586	chr3:118688611-118863998	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11922973	STXBP6	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118688800-118706000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:118689000-118703600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:118692600-118704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:118693400-118704400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:118697200-118703600	Weak transcription	Ovary	ovary
6	chr3:118697400-118702800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:118697400-118704200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:118697400-118704800	Weak transcription	Pancreas	Pancrea
9	chr3:118697600-118704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:118699200-118706000	Enhancers	Brain Substantia Nigra	brain
11	chr3:118700000-118701000	Weak transcription	Brain Anterior Caudate	brain
12	chr3:118700000-118701200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:118700000-118704600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:118700200-118706200	Enhancers	Brain Hippocampus Middle	brain
15	chr3:118700400-118701000	Enhancers	Psoas Muscle	Psoas
16	chr3:118700400-118705800	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:118700400-118706000	Enhancers	Brain Angular Gyrus	brain
18	chr3:118700400-118707800	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:118700600-118700800	Enhancers	Right Atrium	heart
20	chr3:118700600-118700800	Enhancers	K562	blood

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