Variant report

Variant	rs10749863
Chromosome Location	chr1:47174328-47174329
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47155241..47158769-chr1:47172744..47175625,3	MCF-7	breast:
2	chr1:47023201..47026031-chr1:47173277..47176114,2	K562	blood:
3	chr1:47132796..47135398-chr1:47172477..47175917,3	K562	blood:
4	chr1:47133024..47134980-chr1:47172841..47174707,2	K562	blood:
5	chr1:47172743..47174513-chr1:47183253..47185821,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159658	Chromatin interaction
ENSG00000186118	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10749864	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211337	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1258061	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];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794	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]
rs1371834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440487	1.00[ASW][hapmap];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];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473292	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1545206	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595898	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1816730	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs1866770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890473	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];0.90[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083485	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099766	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2165317	1.00[YRI][hapmap]
rs2218191	0.92[EUR][1000 genomes]
rs2476158	0.90[EUR][1000 genomes]
rs35050319	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35861275	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4097354	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4553120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4660359	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4660954	1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601060	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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs618505	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6668899	0.84[ASN][1000 genomes]
rs7516616	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893954	0.83[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10749863	EFCAB14	cis	Esophagus Mucosa	GTEx
rs10749863	ATPAF1	cis	multi-tissue	Pritchard
rs10749863	EFCAB14	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:47154600-47183400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47159200-47182800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:47160600-47181200	Strong transcription	Dnd41	blood
5	chr1:47160800-47175400	Strong transcription	Liver	Liver
6	chr1:47160800-47181800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:47160800-47182200	Strong transcription	Primary B cells from cord blood	blood
8	chr1:47160800-47182200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:47160800-47182400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:47160800-47182600	Strong transcription	Placenta	Placenta
11	chr1:47161200-47182200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr1:47161400-47182200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:47161400-47182800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:47164200-47177400	Strong transcription	GM12878-XiMat	blood
15	chr1:47164400-47182200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:47164400-47182800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:47164600-47181600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:47165600-47182200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:47166200-47182400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:47166600-47177200	Strong transcription	Fetal Brain Female	brain
21	chr1:47166600-47182400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:47166600-47182400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:47166600-47182800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:47166600-47182800	Strong transcription	Fetal Thymus	thymus
25	chr1:47166800-47181800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:47166800-47182200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:47166800-47182400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:47166800-47182600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:47166800-47182800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:47167000-47174400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:47167000-47175400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:47167000-47182400	Strong transcription	Fetal Muscle Leg	muscle
33	chr1:47167000-47182800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:47167200-47175400	Strong transcription	K562	blood
35	chr1:47167200-47180800	Strong transcription	NHEK	skin
36	chr1:47167200-47182600	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:47167400-47182000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:47167600-47183400	Weak transcription	Aorta	Aorta
39	chr1:47168000-47175200	Strong transcription	Osteobl	bone
40	chr1:47168200-47175200	Strong transcription	Fetal Kidney	kidney
41	chr1:47168400-47176600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:47168400-47180600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:47168600-47180800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:47169000-47174600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:47170000-47175200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:47170000-47175200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:47170200-47175400	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:47170400-47177600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:47170600-47177200	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:47170800-47180600	Strong transcription	Duodenum Mucosa	Duodenum

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