Variant report

Variant	rs10800486
Chromosome Location	chr1:169858728-169858729
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000239494	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10733054	0.91[CEU][hapmap]
rs10737549	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs10737551	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs10800479	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10800480	0.96[CEU][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes]
rs10800481	0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10800483	0.96[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10800484	0.85[YRI][hapmap]
rs10800485	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10919239	0.91[CEU][hapmap]
rs10919245	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10919248	0.96[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10919251	0.92[EUR][1000 genomes]
rs10919263	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12133843	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12724797	0.82[JPT][hapmap]
rs1883436	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1883437	0.81[AMR][1000 genomes]
rs2056980	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2056981	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2179396	0.96[CEU][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2281039	0.92[EUR][1000 genomes]
rs2294322	0.92[EUR][1000 genomes]
rs2294496	0.83[YRI][hapmap]
rs2420512	0.92[EUR][1000 genomes]
rs2420514	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2491087	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2491088	0.81[CEU][hapmap]
rs2750016	0.84[CEU][hapmap]
rs2806386	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2806393	0.85[CEU][hapmap]
rs3753308	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766132	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3766134	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs3766137	0.96[CEU][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs3766142	0.95[EUR][1000 genomes]
rs3766144	0.82[YRI][hapmap]
rs3766148	1.00[CEU][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3766151	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3766154	1.00[CEU][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3766155	0.82[CHB][hapmap];0.96[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4141917	0.81[CEU][hapmap]
rs4376791	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4508080	0.96[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4614317	0.96[CEU][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4615900	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4656196	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs4656197	0.82[YRI][hapmap]
rs4656721	0.95[EUR][1000 genomes]
rs4656724	0.82[YRI][hapmap]
rs4656725	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6427220	0.84[CEU][hapmap];0.82[YRI][hapmap]
rs6427224	0.83[YRI][hapmap]
rs6427225	0.96[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6427226	0.90[AFR][1000 genomes]
rs6427227	0.83[YRI][hapmap];0.90[AFR][1000 genomes]
rs6427228	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6656965	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6664099	0.83[YRI][hapmap]
rs6668114	0.90[YRI][hapmap]
rs6669794	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6670818	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671752	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6680508	0.88[CEU][hapmap]
rs6680650	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6682137	0.93[EUR][1000 genomes]
rs6682835	0.96[CEU][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6683056	0.95[CEU][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6687377	0.82[YRI][hapmap]
rs6702969	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs717481	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs732185	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs7525259	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7530237	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7545011	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9287097	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10800486	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs10800486	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
11	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:169847000-169859000	Weak transcription	Left Ventricle	heart
13	chr1:169847200-169860000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:169847200-169860000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:169847400-169860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:169848000-169859000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:169848000-169860000	Weak transcription	HepG2	liver
18	chr1:169848400-169860600	Weak transcription	Fetal Heart	heart
19	chr1:169848800-169859000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:169851600-169859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:169851600-169861200	Weak transcription	Aorta	Aorta
22	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:169851800-169860000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:169852000-169860000	Weak transcription	Lung	lung
25	chr1:169852600-169859000	Weak transcription	Esophagus	oesophagus
26	chr1:169852600-169859000	Weak transcription	Ovary	ovary
27	chr1:169852600-169859200	Weak transcription	Thymus	Thymus
28	chr1:169852600-169859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:169852600-169860000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:169852600-169860000	Weak transcription	Colonic Mucosa	Colon
31	chr1:169852600-169860000	Weak transcription	Gastric	stomach
32	chr1:169852600-169861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:169852600-169861400	Weak transcription	Brain Germinal Matrix	brain
34	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:169852800-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:169853600-169858800	Strong transcription	Primary B cells from cord blood	blood
37	chr1:169853800-169859600	Weak transcription	Fetal Intestine Small	intestine
38	chr1:169853800-169861400	Weak transcription	Fetal Stomach	stomach
39	chr1:169855000-169861400	Weak transcription	HSMMtube	muscle
40	chr1:169855200-169861200	Weak transcription	HSMM	muscle
41	chr1:169855400-169859000	Weak transcription	Pancreas	Pancrea
42	chr1:169855400-169861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:169855600-169859000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:169855600-169860000	Weak transcription	Spleen	Spleen
45	chr1:169855800-169860200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:169856000-169859200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:169856000-169861400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:169856000-169861400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:169856200-169859600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:169856200-169861400	Weak transcription	Brain Angular Gyrus	brain

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