Variant report

Variant	rs4650051
Chromosome Location	chr1:70924020-70924021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10458561	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889869	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10889871	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1145919	0.82[EUR][1000 genomes]
rs11590089	0.87[EUR][1000 genomes]
rs12029858	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1960400	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1967189	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650049	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs473334	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs577476	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs583316	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58977414	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663649	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs9633291	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1002709	chr1:70916210-70939526	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4650051	SRSF11	cis	cerebellum	SCAN
rs4650051	CTH	Cis_1M	lymphoblastoid	RTeQTL
rs4650051	LRRC40	cis	cerebellum	SCAN
rs4650051	LRRIQ3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70909000-70928200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:70917200-70925600	Weak transcription	NHDF-Ad	bronchial
3	chr1:70922800-70925800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:70923200-70924200	Enhancers	Brain Substantia Nigra	brain
5	chr1:70923200-70924400	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:70923200-70924600	Enhancers	Brain Hippocampus Middle	brain
7	chr1:70923200-70924800	Enhancers	Fetal Brain Male	brain
8	chr1:70923400-70924400	Enhancers	Brain Anterior Caudate	brain
9	chr1:70923400-70924400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr1:70923400-70924800	Enhancers	Fetal Brain Female	brain
11	chr1:70923600-70924600	Enhancers	Brain Angular Gyrus	brain
12	chr1:70923800-70924200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:70923800-70924600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:70923800-70924600	Enhancers	K562	blood
15	chr1:70923800-70925600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:70923800-70926000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:70924000-70924400	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:70924000-70924400	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:70924000-70924400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:70924000-70924600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:70924000-70925600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:70924000-70925800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:70924000-70926400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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