Variant report

Variant	rs12794
Chromosome Location	chr1:47141718-47141719
allele	A/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	IRF1	chr1:47141469-47141802	K562	blood:	n/a	chr1:47141620-47141641
2	IRF1	chr1:47141468-47141778	K562	blood:	n/a	chr1:47141620-47141641
3	GATA1	chr1:47141509-47142753	PBDE	blood:	n/a	n/a
4	ATF1	chr1:47141252-47141733	K562	blood:	n/a	n/a
5	SPI1	chr1:47141500-47141735	GM12891	blood:	n/a	n/a
6	IRF1	chr1:47141182-47142625	K562	blood:	n/a	chr1:47141620-47141641

No.	Distal block	Cell Line	Cell type
1	chr1:47133631..47136554-chr1:47137710..47141962,4	K562	blood:
2	chr1:47132879..47135178-chr1:47141656..47143766,2	MCF-7	breast:
3	chr1:47130612..47137538-chr1:47138503..47143012,9	K562	blood:
4	chr1:47134378..47137611-chr1:47139710..47142903,4	MCF-7	breast:
5	chr1:47141197..47146499-chr1:47148014..47152846,8	K562	blood:

Variant related genes	Relation type
ATPAF1	TF binding region
ENSG00000159658	Chromatin interaction
ENSG00000186118	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000233647	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10749863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10749864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211337	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258061	0.82[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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1371834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440487	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[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473292	0.90[YRI][hapmap]
rs1545206	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595898	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1816730	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1866770	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890473	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083485	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099766	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165317	0.90[YRI][hapmap]
rs2218191	0.94[EUR][1000 genomes]
rs2476158	0.92[EUR][1000 genomes]
rs35050319	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861275	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097354	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660359	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4660954	0.90[YRI][hapmap]
rs4660956	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601060	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618505	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668899	0.84[ASN][1000 genomes]
rs7516616	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs12794	EFCAB14	cis	Esophagus Mucosa	GTEx
rs12794	EFCAB14	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134400-47145800	Weak transcription	Hela-S3	cervix
2	chr1:47134400-47147800	Weak transcription	Small Intestine	intestine
3	chr1:47134600-47142600	Weak transcription	HSMMtube	muscle
4	chr1:47134600-47142800	Weak transcription	Ovary	ovary
5	chr1:47134600-47143000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:47134600-47143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:47134600-47145600	Weak transcription	Fetal Kidney	kidney
8	chr1:47134600-47145800	Weak transcription	Fetal Brain Male	brain
9	chr1:47134600-47147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
11	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:47134600-47153000	Weak transcription	Right Atrium	heart
13	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:47134800-47142800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:47134800-47142800	Weak transcription	Fetal Lung	lung
16	chr1:47134800-47143000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:47134800-47143200	Weak transcription	Brain Angular Gyrus	brain
18	chr1:47134800-47152600	Weak transcription	A549	lung
19	chr1:47135000-47142400	Weak transcription	HMEC	breast
20	chr1:47135000-47145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:47135000-47145400	Weak transcription	Esophagus	oesophagus
22	chr1:47138000-47152000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:47138200-47147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:47138200-47152200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:47138200-47152600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
28	chr1:47138400-47147800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:47138400-47151600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:47138400-47152200	Strong transcription	Adipose Nuclei	Adipose
31	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:47138600-47152400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr1:47138800-47143600	Strong transcription	Pancreas	Pancrea
35	chr1:47138800-47152800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr1:47138800-47153200	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
38	chr1:47139000-47142800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:47139000-47145800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:47139000-47148400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:47139000-47152400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:47139000-47152800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr1:47139200-47141800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:47139200-47145200	Weak transcription	Gastric	stomach
46	chr1:47139200-47147400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:47139200-47153000	Weak transcription	Fetal Heart	heart
48	chr1:47139200-47153400	Strong transcription	Dnd41	blood
49	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
50	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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