Variant report

Variant	rs12047487
Chromosome Location	chr1:169850666-169850667
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169847146..169850317-chr1:169850331..169854277,4	K562	blood:
2	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10737550	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10737551	0.88[CEU][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10800480	0.86[YRI][hapmap]
rs10800481	0.86[YRI][hapmap]
rs10800483	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs10800484	0.88[CEU][hapmap];0.82[CHB][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10919248	0.86[YRI][hapmap]
rs10919257	0.84[EUR][1000 genomes]
rs10919263	0.80[AFR][1000 genomes]
rs12133843	0.85[YRI][hapmap]
rs2143122	0.84[EUR][1000 genomes]
rs2179396	0.86[YRI][hapmap]
rs2294496	0.89[CEU][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2901179	0.85[EUR][1000 genomes]
rs3766137	0.91[YRI][hapmap]
rs3766144	0.88[CEU][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3766148	0.85[YRI][hapmap]
rs3766154	0.86[YRI][hapmap]
rs3766155	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs4508080	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs4614317	0.86[YRI][hapmap]
rs4656197	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4656199	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4656200	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4656724	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs508063	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs603246	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs6427220	0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs6427224	0.89[CEU][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6427225	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs6427226	0.85[CHB][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6427227	0.93[CEU][hapmap];0.86[CHB][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6664099	0.93[CEU][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6668114	0.85[CEU][hapmap];0.84[YRI][hapmap];0.85[EUR][1000 genomes]
rs6669794	0.80[AFR][1000 genomes]
rs6680938	0.83[EUR][1000 genomes]
rs6682835	0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs6683056	0.85[YRI][hapmap]
rs6684481	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6687377	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6702969	0.86[AFR][1000 genomes]
rs7521700	0.92[CEU][hapmap]
rs7525259	0.85[YRI][hapmap]
rs7530237	0.90[YRI][hapmap]
rs9287097	0.85[YRI][hapmap]

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
rs12047487	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	chr1:169842200-169857400	Weak transcription	Fetal Brain Male	brain
5	chr1:169842400-169850800	Weak transcription	Esophagus	oesophagus
6	chr1:169842400-169851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:169842400-169851000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:169842400-169855600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:169842600-169854800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:169843000-169851000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:169843600-169855000	Weak transcription	NHEK	skin
13	chr1:169843800-169850800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:169844000-169851200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:169844000-169851200	Weak transcription	Pancreas	Pancrea
16	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:169844400-169857400	Weak transcription	K562	blood
18	chr1:169844800-169851200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:169844800-169854600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:169844800-169855400	Weak transcription	Hela-S3	cervix
21	chr1:169844800-169856000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:169845000-169854000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:169845200-169850800	Weak transcription	Brain Germinal Matrix	brain
25	chr1:169845200-169850800	Weak transcription	Lung	lung
26	chr1:169845200-169851000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:169845200-169851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:169845200-169853800	Weak transcription	Fetal Kidney	kidney
29	chr1:169845200-169854400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:169845200-169855000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:169845200-169857200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:169845200-169857200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:169845200-169857400	Weak transcription	HUVEC	blood vessel
34	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
35	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:169845400-169853400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
39	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:169845600-169855000	Weak transcription	Fetal Brain Female	brain
41	chr1:169845800-169855600	Weak transcription	A549	lung
42	chr1:169846000-169854600	Weak transcription	HSMMtube	muscle
43	chr1:169846000-169858000	Weak transcription	Small Intestine	intestine
44	chr1:169846600-169851000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:169846600-169851000	Weak transcription	Fetal Intestine Small	intestine
46	chr1:169846600-169851000	Weak transcription	Fetal Stomach	stomach
47	chr1:169847000-169850800	Weak transcription	Aorta	Aorta
48	chr1:169847000-169852000	Weak transcription	Ovary	ovary
49	chr1:169847000-169859000	Weak transcription	Left Ventricle	heart
50	chr1:169847200-169855600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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