Variant report

Variant	rs12048954
Chromosome Location	chr1:47146408-47146409
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	chr1:47137606..47140204-chr1:47144038..47147459,3	K562	blood:
2	chr1:47141197..47146499-chr1:47148014..47152846,8	K562	blood:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction
ENSG00000228237	Chromatin interaction
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10890409	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10890413	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211339	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211351	0.83[EUR][1000 genomes]
rs11211353	0.82[AFR][1000 genomes]
rs1139759	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12026027	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs12029031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038572	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12118483	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138338	0.82[EUR][1000 genomes]
rs12142631	0.82[EUR][1000 genomes]
rs12733214	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440484	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007344	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083486	0.85[JPT][hapmap]
rs2218190	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737729	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660950	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660957	0.89[CEU][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs620913	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12048954	C1orf210	cis	cerebellum	SCAN
rs12048954	ATPAF1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134400-47147800	Weak transcription	Small Intestine	intestine
2	chr1:47134600-47147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
4	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:47134600-47153000	Weak transcription	Right Atrium	heart
6	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:47134800-47152600	Weak transcription	A549	lung
8	chr1:47138000-47152000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:47138200-47147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:47138200-47152200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:47138200-47152600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
14	chr1:47138400-47147800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:47138400-47151600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:47138400-47152200	Strong transcription	Adipose Nuclei	Adipose
17	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:47138600-47152400	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:47138800-47152800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:47138800-47153200	Strong transcription	Fetal Muscle Leg	muscle
22	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
23	chr1:47139000-47148400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:47139000-47152400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:47139000-47152800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:47139200-47147400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:47139200-47153000	Weak transcription	Fetal Heart	heart
29	chr1:47139200-47153400	Strong transcription	Dnd41	blood
30	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
31	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:47139400-47146800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:47139400-47152600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:47139400-47152600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:47139400-47153000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:47139600-47152800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:47139600-47153000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:47139800-47147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:47139800-47152800	Strong transcription	Osteobl	bone
42	chr1:47140000-47155400	Strong transcription	HSMM	muscle
43	chr1:47140600-47147000	Strong transcription	Fetal Intestine Large	intestine
44	chr1:47141000-47147800	Strong transcription	Brain Anterior Caudate	brain
45	chr1:47141000-47147800	Weak transcription	Lung	lung
46	chr1:47141200-47146600	Strong transcription	Brain Substantia Nigra	brain
47	chr1:47141200-47150800	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:47141200-47157800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:47141600-47147000	Strong transcription	HUVEC	blood vessel

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