Variant report

Variant	rs11808053
Chromosome Location	chr1:154749047-154749048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154736362..154738572-chr1:154746811..154749808,2	K562	blood:
2	chr1:154744584..154747460-chr1:154748764..154751620,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10752608	0.81[ASN][1000 genomes]
rs10908438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10908439	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908441	0.83[ASN][1000 genomes]
rs11264257	0.80[ASN][1000 genomes]
rs11584403	0.81[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap]
rs11589471	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047201	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845391	0.81[JPT][hapmap]
rs56995760	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60161870	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6426929	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs6666341	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532286	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs7547552	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
3	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11808053	RPTN	cis	cerebellum	SCAN
rs11808053	HIST2H2BE	cis	parietal	SCAN
rs11808053	ROBLD3	cis	cerebellum	SCAN
rs11808053	ZNF687	cis	cerebellum	SCAN
rs11808053	LCE3C	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154740800-154764000	Weak transcription	Right Ventricle	heart
2	chr1:154742200-154751400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:154744800-154749200	Enhancers	Brain Anterior Caudate	brain
4	chr1:154744800-154749400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:154745000-154758200	Weak transcription	Colonic Mucosa	Colon
6	chr1:154745200-154750600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr1:154745600-154749200	Enhancers	Fetal Muscle Leg	muscle
8	chr1:154746200-154759600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:154746600-154757400	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:154746600-154763800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:154746800-154749400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:154747200-154749200	Enhancers	Fetal Brain Female	brain
13	chr1:154747400-154757400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:154747600-154749600	Enhancers	Fetal Brain Male	brain
15	chr1:154747800-154751400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:154747800-154757000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:154748000-154749200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:154748000-154751800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:154748200-154749200	Enhancers	Fetal Thymus	thymus
20	chr1:154748600-154749200	Enhancers	Liver	Liver
21	chr1:154748600-154749400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:154748600-154749400	Weak transcription	Fetal Stomach	stomach
23	chr1:154748600-154750200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:154748600-154752000	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:154748800-154749200	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:154748800-154749200	Enhancers	Fetal Muscle Trunk	muscle
27	chr1:154748800-154750000	Weak transcription	GM12878-XiMat	blood
28	chr1:154748800-154750200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:154748800-154760600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:154748800-154764000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:154749000-154749200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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