Variant report

Variant	rs3766155
Chromosome Location	chr1:169859717-169859718
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:169859666-169859843	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169858457..169860973-chr1:169907396..169909921,2	MCF-7	breast:
2	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
3	chr1:169827363..169830253-chr1:169858202..169860051,2	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000239494	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10737549	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs10737550	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10737551	0.96[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10800479	0.83[AFR][1000 genomes]
rs10800480	0.91[YRI][hapmap]
rs10800481	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs10800483	0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs10800484	0.96[CEU][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10800486	0.82[CHB][hapmap];0.96[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10919245	0.82[AFR][1000 genomes]
rs10919248	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs10919257	0.90[EUR][1000 genomes]
rs10919263	0.97[AFR][1000 genomes]
rs12047487	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs12133843	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs1883436	0.90[AFR][1000 genomes]
rs2143122	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2179396	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs2294496	0.96[CEU][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2420514	0.83[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs2901179	0.91[EUR][1000 genomes]
rs3753308	0.96[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3766137	0.87[YRI][hapmap]
rs3766144	0.96[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3766148	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs3766154	0.91[YRI][hapmap];0.98[AFR][1000 genomes]
rs4376791	0.81[AFR][1000 genomes]
rs4508080	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs4614317	0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs4656197	1.00[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656199	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656200	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656724	1.00[CEU][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508063	0.85[CEU][hapmap]
rs603246	0.82[CEU][hapmap]
rs6427220	0.87[YRI][hapmap];0.91[EUR][1000 genomes]
rs6427224	0.96[CEU][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6427225	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs6427226	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6427227	1.00[CEU][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6427228	0.83[AFR][1000 genomes]
rs6656965	0.90[AFR][1000 genomes]
rs6664099	1.00[CEU][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6668114	0.92[CEU][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes]
rs6669794	0.84[AFR][1000 genomes]
rs6670818	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6671752	0.83[AFR][1000 genomes]
rs6680650	0.82[AFR][1000 genomes]
rs6680938	0.89[EUR][1000 genomes]
rs6682835	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs6683056	0.91[YRI][hapmap];0.94[AFR][1000 genomes]
rs6684481	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6687377	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6702969	0.92[AFR][1000 genomes]
rs717481	0.90[AFR][1000 genomes]
rs7521700	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7525259	0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs7530237	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs7545011	0.81[AFR][1000 genomes]
rs9287097	0.91[YRI][hapmap];0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3766155	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
3	chr1:169833800-169860200	Weak transcription	HMEC	breast
4	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
8	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
10	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:169847200-169860000	Weak transcription	Brain Substantia Nigra	brain
12	chr1:169847200-169860000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:169847400-169860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:169848000-169860000	Weak transcription	HepG2	liver
15	chr1:169848400-169860600	Weak transcription	Fetal Heart	heart
16	chr1:169851600-169859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:169851600-169861200	Weak transcription	Aorta	Aorta
18	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:169851800-169860000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:169852000-169860000	Weak transcription	Lung	lung
21	chr1:169852600-169859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:169852600-169860000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:169852600-169860000	Weak transcription	Colonic Mucosa	Colon
24	chr1:169852600-169860000	Weak transcription	Gastric	stomach
25	chr1:169852600-169861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:169852600-169861400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:169852800-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:169853800-169861400	Weak transcription	Fetal Stomach	stomach
30	chr1:169855000-169861400	Weak transcription	HSMMtube	muscle
31	chr1:169855200-169861200	Weak transcription	HSMM	muscle
32	chr1:169855400-169861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:169855600-169860000	Weak transcription	Spleen	Spleen
34	chr1:169855800-169860200	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr1:169856000-169861400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:169856000-169861400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:169856200-169861400	Weak transcription	Brain Angular Gyrus	brain
38	chr1:169856400-169859800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:169856400-169860000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:169857400-169860000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:169857400-169860400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:169857400-169861400	Weak transcription	Fetal Brain Female	brain
43	chr1:169857600-169860000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:169857600-169860800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:169857600-169861200	Weak transcription	Hela-S3	cervix
46	chr1:169857800-169860000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr1:169857800-169860000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:169857800-169860000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr1:169857800-169860200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:169857800-169860200	Weak transcription	NH-A	brain

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