Variant report

Variant	rs10749864
Chromosome Location	chr1:47185988-47185989
allele	C/T
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	JUN	chr1:47183215-47186038	K562	blood:	n/a	chr1:47184831-47184840 chr1:47184852-47184861 chr1:47184848-47184861 chr1:47184512-47184521

No.	Distal block	Cell Line	Cell type
1	chr1:47133847..47136859-chr1:47183270..47186412,3	K562	blood:
2	chr1:47132021..47134292-chr1:47182751..47186267,3	MCF-7	breast:
3	chr1:47131887..47139340-chr1:47181784..47186573,11	K562	blood:

Variant related genes	Relation type
EFCAB14	TF binding region
ENSG00000123472	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000186118	Chromatin interaction

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

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

rs_ID	r²[population]
rs10749863	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789491	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211337	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211342	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1258061	0.93[EUR][1000 genomes]
rs12794	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1371834	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1440487	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1545206	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1595898	0.81[EUR][1000 genomes]
rs1866770	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1890473	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2083485	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2099766	0.81[EUR][1000 genomes]
rs2218191	0.87[EUR][1000 genomes]
rs2476158	0.86[EUR][1000 genomes]
rs35050319	0.93[EUR][1000 genomes]
rs35861275	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4097354	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4553120	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660956	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs601060	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs618505	0.87[EUR][1000 genomes]
rs7516616	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7547522	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[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
rs10749864	EFCAB14	cis	Whole Blood	GTEx
rs10749864	EFCAB14	cis	Esophagus Mucosa	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47185200-47189600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:47185200-47189800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:47185400-47186000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:47185600-47187200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:47185600-47188000	Enhancers	Stomach Mucosa	stomach
6	chr1:47185600-47188400	Weak transcription	Psoas Muscle	Psoas
7	chr1:47185600-47190600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:47185600-47190600	Weak transcription	Brain Anterior Caudate	brain
9	chr1:47185800-47186000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:47185800-47186000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:47185800-47186800	Weak transcription	K562	blood
12	chr1:47185800-47188400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:47185800-47188600	Weak transcription	Adipose Nuclei	Adipose
14	chr1:47185800-47190200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:47185800-47190200	Weak transcription	Lung	lung
16	chr1:47185800-47190200	Weak transcription	Right Ventricle	heart
17	chr1:47185800-47190200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:47185800-47190400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:47185800-47190400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:47185800-47190400	Weak transcription	Left Ventricle	heart
21	chr1:47185800-47190400	Weak transcription	HepG2	liver
22	chr1:47185800-47190600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:47185800-47190600	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:47185800-47190600	Weak transcription	Brain Angular Gyrus	brain
25	chr1:47185800-47190600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:47185800-47190600	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:47185800-47190600	Weak transcription	Fetal Lung	lung
28	chr1:47185800-47190600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:47185800-47190600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:47185800-47190600	Weak transcription	Hela-S3	cervix
31	chr1:47185800-47190600	Weak transcription	HMEC	breast
32	chr1:47185800-47190600	Weak transcription	NHEK	skin
33	chr1:47185800-47190800	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:47185800-47190800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:47185800-47194000	Weak transcription	Fetal Intestine Small	intestine
36	chr1:47185800-47194200	Weak transcription	Right Atrium	heart

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