Variant report

Variant	rs7740081
Chromosome Location	chr6:73973719-73973720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:73972509-73976913	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:73973719-73973769	AoSMC	blood vessel:	n/a
2	chr6:73973719-73973769	IMR90	lung:	fetal
3	chr6:73973719-73973769	AG09319	gingival:	n/a
4	chr6:73973719-73973769	GM06990	blood:	n/a
5	chr6:73973719-73973769	HCF	heart:	n/a
6	chr6:73973719-73973769	SAEC	small airway:	n/a
7	chr6:73973719-73973769	HL-60	blood:	n/a
8	chr6:73973719-73973769	HIPEpiC	eye:	n/a
9	chr6:73973719-73973769	HEEpiC	esophagus:	n/a
10	chr6:73973719-73973769	HUVEC	blood vessel:	n/a
11	chr6:73973719-73973769	HEK293	kidney:	embryo
12	chr6:73973719-73973769	HMEC	breast:	n/a
13	chr6:73973719-73973769	Caco-2	colon:	n/a
14	chr6:73973719-73973769	HPAEpiC	pulmonary alveolar:	n/a
15	chr6:73973719-73973769	RPTEC	kidney:	n/a
16	chr6:73973719-73973769	PANC-1	pancreas:	n/a
17	chr6:73973719-73973769	Hepatocyte	liver:	n/a
18	chr6:73973719-73973769	GM19239	blood:	n/a
19	chr6:73973719-73973769	HAEpiC	amniotic membrane:	n/a
20	chr6:73973719-73973769	AG04450	lung:	fetal
21	chr6:73973719-73973769	SK-N-SH_RA	brain:	n/a
22	chr6:73973719-73973769	NB4	blood:	n/a
23	chr6:73973719-73973769	AG04449	skin:	fetal
24	chr6:73973719-73973769	HRCEpiC	kidney:	n/a
25	chr6:73973719-73973769	HCM	heart:	n/a
26	chr6:73973719-73973769	MCF10A-Er-Src	breast:	n/a
27	chr6:73973719-73973769	ovcar-3	ovarian:	n/a
28	chr6:73973719-73973769	U87	brain:	n/a
29	chr6:73973719-73973769	SK-N-SH	brain:	n/a
30	chr6:73973719-73973769	ProgFib	skin:	n/a
31	chr6:73973719-73973769	AG10803	skin:	n/a
32	chr6:73973719-73973769	ECC-1	luminal epithelium:	n/a
33	chr6:73973719-73973769	SK-N-MC	brain:	n/a
34	chr6:73973719-73973769	H1-hESC	embryonic stem cell:	embryo
35	chr6:73973719-73973769	SKMC	muscle:	n/a
36	chr6:73973719-73973769	Jurkat	blood:	n/a
37	chr6:73973719-73973769	CMK	blood:	n/a
38	chr6:73973719-73973769	NHBE	bronchial:	n/a
39	chr6:73973719-73973769	PFSK-1	brain:	n/a
40	chr6:73973719-73973769	Hela-S3	cervix:	n/a
41	chr6:73973719-73973769	HCPEpiC	choroid plexus:	n/a
42	chr6:73973719-73973769	HRE	kidney:	n/a
43	chr6:73973719-73973769	MCF-7	breast:	n/a
44	chr6:73973719-73973769	GM12891	blood:	n/a
45	chr6:73973719-73973769	T-47D	breast:	n/a
46	chr6:73973719-73973769	HNPCEpiC	eye:	n/a
47	chr6:73973719-73973769	A549	lung:	n/a
48	chr6:73973719-73973769	HCT-116	colon:	n/a
49	chr6:73973719-73973769	HRPEpiC	eye:	n/a
50	chr6:73973719-73973769	NHDF-neo	bronchial:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:73972686..73974360-chr6:74230027..74232988,2	MCF-7	breast:
2	chr6:73968889..73971935-chr6:73973198..73976161,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000229852	TF binding region
KHDC1	TF binding region
ENSG00000243501	TF binding region
KHDC1	CpG island
ENSG00000229852	CpG island
ENSG00000243501	CpG island
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10455092	0.92[ASN][1000 genomes]
rs10455273	0.92[ASN][1000 genomes]
rs10455274	0.92[ASN][1000 genomes]
rs1066687	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12153835	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12203663	0.92[ASN][1000 genomes]
rs12208781	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12210531	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12216162	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12526643	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12529624	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529658	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12530029	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12530079	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13194683	0.91[ASN][1000 genomes]
rs13212903	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213885	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219250	0.92[ASN][1000 genomes]
rs1555443	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869559	0.94[ASN][1000 genomes]
rs1970551	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974368	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124004	0.91[ASN][1000 genomes]
rs2124006	0.84[ASN][1000 genomes]
rs2168113	0.94[ASN][1000 genomes]
rs2254630	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603471	0.96[ASN][1000 genomes]
rs2797086	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28530192	0.92[ASN][1000 genomes]
rs2984129	0.92[ASN][1000 genomes]
rs34246858	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34531450	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34637067	0.92[ASN][1000 genomes]
rs34821383	0.92[ASN][1000 genomes]
rs35664677	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706533	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706534	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708042	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471270	0.96[ASN][1000 genomes]
rs471938	0.92[ASN][1000 genomes]
rs502107	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502282	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510551	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511219	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs512366	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555779	0.91[ASN][1000 genomes]
rs57113415	0.83[ASN][1000 genomes]
rs573535	0.92[ASN][1000 genomes]
rs576229	0.90[ASN][1000 genomes]
rs579736	0.96[ASN][1000 genomes]
rs61493410	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438232	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438233	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438235	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438239	0.92[ASN][1000 genomes]
rs66984567	0.92[ASN][1000 genomes]
rs6923111	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6923734	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7382700	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7742847	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743609	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744174	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758047	0.94[ASN][1000 genomes]
rs7759043	0.94[ASN][1000 genomes]
rs7759315	0.94[ASN][1000 genomes]
rs7764719	0.91[ASN][1000 genomes]
rs7765618	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769905	0.86[ASN][1000 genomes]
rs9800483	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9800824	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1030079	chr6:73920050-73984084	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7740081	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7740081	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73971800-73973800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:73971800-73973800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:73971800-73973800	Active TSS	Brain Hippocampus Middle	brain
4	chr6:73971800-73974000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:73971800-73974000	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:73971800-73974600	Active TSS	Brain Angular Gyrus	brain
7	chr6:73972000-73973800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:73972000-73973800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:73972000-73973800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:73972000-73974600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:73972200-73973800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:73972200-73973800	Active TSS	Fetal Kidney	kidney
13	chr6:73972200-73974000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:73972200-73974200	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr6:73972400-73973800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr6:73972400-73973800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:73972400-73973800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr6:73972400-73973800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:73972400-73973800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:73972400-73973800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr6:73972400-73974000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:73972400-73974200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr6:73972600-73973800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:73972600-73974000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr6:73972600-73974000	Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:73972600-73974800	Enhancers	Stomach Mucosa	stomach
27	chr6:73973000-73973800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:73973000-73973800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr6:73973000-73973800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr6:73973000-73973800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr6:73973000-73973800	Flanking Active TSS	Fetal Thymus	thymus
32	chr6:73973000-73973800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr6:73973000-73974200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:73973000-73974200	Flanking Active TSS	HMEC	breast
35	chr6:73973000-73974400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr6:73973200-73973800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:73973200-73973800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:73973200-73973800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr6:73973200-73973800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:73973200-73973800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr6:73973200-73973800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr6:73973200-73973800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:73973200-73973800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr6:73973200-73973800	Flanking Active TSS	Fetal Brain Male	brain
45	chr6:73973200-73973800	Flanking Active TSS	Fetal Heart	heart
46	chr6:73973200-73973800	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr6:73973200-73973800	Flanking Active TSS	Fetal Stomach	stomach
48	chr6:73973200-73973800	Flanking Active TSS	Hela-S3	cervix
49	chr6:73973200-73974000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:73973200-73974200	Flanking Active TSS	GM12878-XiMat	blood

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