Variant report

Variant	rs9811107
Chromosome Location	chr3:155474879-155474880
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	chr3:155468097..155470070-chr3:155473602..155476572,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf33-1	chr3:155474205-155475125	l_2508_chr3:155472774-155475125_lung

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13061403	0.87[AFR][1000 genomes]
rs13066198	0.87[AFR][1000 genomes]
rs13095901	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13096944	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13099457	0.92[AFR][1000 genomes]
rs13325975	0.90[EUR][1000 genomes]
rs1695518	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2201932	0.84[CHD][hapmap]
rs34317674	0.92[AFR][1000 genomes]
rs35582521	0.87[AFR][1000 genomes]
rs35769564	0.82[ASN][1000 genomes]
rs358699	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs358700	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs358731	0.90[EUR][1000 genomes]
rs358734	0.98[GIH][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs35963081	0.88[ASN][1000 genomes]
rs369155	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs378211	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs400999	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs426236	0.81[CHB][hapmap];0.86[MEX][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs442774	0.90[EUR][1000 genomes]
rs4680216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6441012	0.81[AFR][1000 genomes]
rs6774542	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[ASN][1000 genomes]
rs6794117	0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6806798	0.94[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73159012	0.82[ASN][1000 genomes]
rs7615604	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7642920	0.94[ASW][hapmap];0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs7653384	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9864027	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9866823	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv592079	chr3:155474879-155493915	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9811107	PLCH1	cis	cerebellum	SCAN
rs9811107	SMC4	cis	cerebellum	SCAN
rs9811107	C3orf33	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155463800-155475200	Weak transcription	Left Ventricle	heart
2	chr3:155463800-155487800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
4	chr3:155464000-155476600	Weak transcription	Ovary	ovary
5	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
8	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
10	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:155466400-155484600	Weak transcription	Fetal Brain Male	brain
14	chr3:155467000-155487200	Weak transcription	Fetal Brain Female	brain
15	chr3:155467200-155478400	Weak transcription	Fetal Intestine Large	intestine
16	chr3:155467200-155479400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:155467200-155500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:155467200-155508000	Weak transcription	K562	blood
19	chr3:155467200-155508800	Weak transcription	Hela-S3	cervix
20	chr3:155467400-155481600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:155467400-155508400	Weak transcription	HepG2	liver
22	chr3:155468000-155487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:155469400-155481600	Weak transcription	Liver	Liver
24	chr3:155470000-155478800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:155470200-155483000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:155470400-155487400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:155470400-155487600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:155470800-155487400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:155471000-155481400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:155471000-155487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:155471000-155487800	Weak transcription	Right Ventricle	heart
32	chr3:155471200-155487600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr3:155471400-155509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:155471800-155487600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:155472200-155487600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:155472400-155487200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:155472800-155488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:155472800-155500000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:155473200-155487400	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:155473200-155487400	Weak transcription	Thymus	Thymus
41	chr3:155474200-155487600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:155474200-155487800	Weak transcription	Spleen	Spleen
43	chr3:155474200-155490600	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:155474200-155497600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:155474400-155492000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:155474800-155476600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:155474800-155487400	Weak transcription	Dnd41	blood
48	chr3:155474800-155487800	Weak transcription	Primary T cells from cord blood	blood
49	chr3:155474800-155489000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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