Variant report

Variant	rs2275380
Chromosome Location	chr1:47147728-47147729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47139387..47141450-chr1:47147658..47149516,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228237	Chromatin interaction
ENSG00000123472	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	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10890412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10890413	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211340	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211351	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1139759	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[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];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038572	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12048954	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]
rs12118483	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138338	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12142631	0.83[EUR][1000 genomes]
rs12733214	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1440484	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007344	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083486	0.85[JPT][hapmap]
rs2218190	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737729	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766224	0.80[CHB][hapmap]
rs4660950	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660957	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs620913	0.81[CHB][hapmap];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
rs2275380	C1orf210	cis	cerebellum	SCAN
rs2275380	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	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
3	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:47134600-47153000	Weak transcription	Right Atrium	heart
5	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:47134800-47152600	Weak transcription	A549	lung
7	chr1:47138000-47152000	Strong transcription	Stomach Smooth Muscle	stomach
8	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:47138200-47152200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:47138200-47152600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
12	chr1:47138400-47147800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:47138400-47151600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:47138400-47152200	Strong transcription	Adipose Nuclei	Adipose
15	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:47138600-47152400	Strong transcription	Primary hematopoietic stem cells	blood
18	chr1:47138800-47152800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:47138800-47153200	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
21	chr1:47139000-47148400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:47139000-47152400	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:47139000-47152800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:47139200-47153000	Weak transcription	Fetal Heart	heart
26	chr1:47139200-47153400	Strong transcription	Dnd41	blood
27	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
28	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:47139400-47152600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:47139400-47152600	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:47139400-47153000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:47139600-47152800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:47139600-47153000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:47139800-47147800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:47139800-47152800	Strong transcription	Osteobl	bone
38	chr1:47140000-47155400	Strong transcription	HSMM	muscle
39	chr1:47141000-47147800	Strong transcription	Brain Anterior Caudate	brain
40	chr1:47141000-47147800	Weak transcription	Lung	lung
41	chr1:47141200-47150800	Strong transcription	Brain Hippocampus Middle	brain
42	chr1:47141200-47157800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:47142000-47147800	Weak transcription	Stomach Mucosa	stomach
45	chr1:47142000-47153000	Strong transcription	Liver	Liver
46	chr1:47142000-47159400	Strong transcription	K562	blood
47	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:47142400-47151000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:47142400-47158000	Strong transcription	HMEC	breast
50	chr1:47142600-47150800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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