Variant report

Variant	rs510551
Chromosome Location	chr6:73972946-73972947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:250)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:250 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:73972390-73973095	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:73972651-73973190	HL-60	blood:	n/a	n/a
3	POLR2A	chr6:73972563-73973188	MCF10A-Er-Src	breast:	n/a	n/a
4	YY1	chr6:73972770-73973280	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:73971964-73973411	SK-N-MC	brain:	n/a	n/a
6	STAT1	chr6:73972689-73973132	GM12878	blood:	n/a	n/a
7	HMGN3	chr6:73972582-73973199	K562	blood:	n/a	n/a
8	CHD1	chr6:73972429-73973323	GM12878	blood:	n/a	n/a
9	GABPA	chr6:73972297-73973345	SK-N-SH	brain:	n/a	n/a
10	MAX	chr6:73972458-73973295	MCF-7	breast:	n/a	n/a
11	TAF1	chr6:73972814-73973132	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr6:73972431-73973415	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr6:73972759-73973204	SK-N-SH	brain:	n/a	n/a
14	CHD2	chr6:73972487-73973068	H1-hESC	embryonic stem cell:	n/a	n/a
15	ELF1	chr6:73972799-73973211	K562	blood:	n/a	n/a
16	POLR2A	chr6:73972370-73973219	SK-N-SH	brain:	n/a	n/a
17	RAD21	chr6:73972890-73973092	SK-N-SH_RA	brain:	n/a	n/a
18	SPI1	chr6:73972836-73972971	K562	blood:	n/a	n/a
19	TAF1	chr6:73972739-73973140	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr6:73972880-73973030	HMEC	breast:	n/a	n/a
21	ZBTB7A	chr6:73972760-73973452	K562	blood:	n/a	n/a
22	CTCF	chr6:73972936-73973170	GM19240	blood:	n/a	n/a
23	CTCF	chr6:73972940-73973090	NHLF	lung:	n/a	n/a
24	POLR2A	chr6:73972596-73973172	Hela-S3	cervix:	n/a	n/a
25	MAX	chr6:73972508-73973602	H1-hESC	embryonic stem cell:	n/a	chr6:73973333-73973343
26	POLR2A	chr6:73972389-73973425	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:73972645-73973165	HUVEC	blood vessel:	n/a	n/a
28	MYC	chr6:73972369-73973186	K562	blood:	n/a	n/a
29	CTCF	chr6:73972831-73973196	IMR90	lung:	n/a	n/a
30	PML	chr6:73972223-73973394	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:73972469-73973319	GM12892	blood:	n/a	n/a
32	CTCF	chr6:73972920-73973070	GM12868	blood:	n/a	n/a
33	POLR2A	chr6:73972680-73973227	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr6:73972468-73973305	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr6:73972677-73973251	GM12892	blood:	n/a	n/a
36	GABPA	chr6:73972478-73973318	MCF-7	breast:	n/a	n/a
37	CTCF	chr6:73972800-73972950	GM12867	blood:	n/a	n/a
38	MAX	chr6:73972573-73973276	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr6:73972663-73973226	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr6:73972678-73973179	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr6:73972560-73973214	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:73972784-73973196	K562	blood:	n/a	n/a
43	POLR2A	chr6:73972529-73973155	GM12878	blood:	n/a	n/a
44	MAX	chr6:73972711-73973641	H1-hESC	embryonic stem cell:	n/a	chr6:73973333-73973343
45	MAZ	chr6:73972817-73973537	GM12878	blood:	n/a	chr6:73973333-73973343
46	YY1	chr6:73972476-73973136	K562	blood:	n/a	n/a
47	POLR2A	chr6:73972635-73973254	MCF-7	breast:	n/a	n/a
48	ELK1	chr6:73972895-73973106	K562	blood:	n/a	n/a
49	TBP	chr6:73972827-73973082	GM12878	blood:	n/a	n/a
50	MXI1	chr6:73972567-73973166	Hela-S3	cervix:	n/a	n/a

No data

(count:1 , 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:

No data

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

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10455092	0.91[ASN][1000 genomes]
rs10455273	0.91[ASN][1000 genomes]
rs10455274	0.91[ASN][1000 genomes]
rs1066687	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12153835	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203663	0.91[ASN][1000 genomes]
rs12208781	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12210531	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12216162	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12526643	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12529624	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12529658	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12530029	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12530079	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13194683	0.89[ASN][1000 genomes]
rs13212903	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13213885	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13219250	0.91[ASN][1000 genomes]
rs1555443	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869559	0.92[ASN][1000 genomes]
rs1970551	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1974368	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124004	0.89[ASN][1000 genomes]
rs2168113	0.92[ASN][1000 genomes]
rs2254630	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2603471	0.94[ASN][1000 genomes]
rs2797086	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28530192	0.91[ASN][1000 genomes]
rs2984129	0.91[ASN][1000 genomes]
rs34246858	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34531450	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34637067	0.91[ASN][1000 genomes]
rs34821383	0.91[ASN][1000 genomes]
rs35664677	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4706533	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4706534	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4708041	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4708042	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs471270	0.94[ASN][1000 genomes]
rs471938	0.91[ASN][1000 genomes]
rs502107	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs502282	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509406	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511219	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512366	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555779	0.89[ASN][1000 genomes]
rs57113415	0.82[ASN][1000 genomes]
rs573535	0.91[ASN][1000 genomes]
rs576229	0.88[ASN][1000 genomes]
rs579736	0.94[ASN][1000 genomes]
rs61493410	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62438232	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62438233	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62438235	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62438239	0.91[ASN][1000 genomes]
rs66984567	0.91[ASN][1000 genomes]
rs6923111	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6923734	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7382700	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7740081	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7742847	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7743609	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7744174	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7758047	0.92[ASN][1000 genomes]
rs7759043	0.92[ASN][1000 genomes]
rs7759315	0.92[ASN][1000 genomes]
rs7764719	0.87[ASN][1000 genomes]
rs7765618	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7769905	0.85[ASN][1000 genomes]
rs9800483	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9800824	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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
rs510551	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx
rs510551	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73971800-73973000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:73971800-73973200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:73971800-73973200	Active TSS	Brain Germinal Matrix	brain
4	chr6:73971800-73973400	Active TSS	Rectal Smooth Muscle	rectum
5	chr6:73971800-73973400	Active TSS	NHDF-Ad	bronchial
6	chr6:73971800-73973400	Active TSS	Osteobl	bone
7	chr6:73971800-73973600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr6:73971800-73973600	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr6:73971800-73973800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr6:73971800-73973800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:73971800-73973800	Active TSS	Brain Hippocampus Middle	brain
12	chr6:73971800-73974000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:73971800-73974000	Active TSS	Brain Cingulate Gyrus	brain
14	chr6:73971800-73974600	Active TSS	Brain Angular Gyrus	brain
15	chr6:73972000-73973000	Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr6:73972000-73973000	Active TSS	Duodenum Mucosa	Duodenum
17	chr6:73972000-73973200	Active TSS	Fetal Brain Male	brain
18	chr6:73972000-73973200	Active TSS	NH-A	brain
19	chr6:73972000-73973400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr6:73972000-73973400	Active TSS	Brain Substantia Nigra	brain
21	chr6:73972000-73973400	Active TSS	Psoas Muscle	Psoas
22	chr6:73972000-73973400	Active TSS	Stomach Smooth Muscle	stomach
23	chr6:73972000-73973600	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:73972000-73973800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:73972000-73973800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:73972000-73973800	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:73972000-73974600	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:73972200-73973000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:73972200-73973000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:73972200-73973000	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr6:73972200-73973000	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:73972200-73973200	Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr6:73972200-73973200	Active TSS	Fetal Intestine Large	intestine
34	chr6:73972200-73973200	Active TSS	Fetal Stomach	stomach
35	chr6:73972200-73973400	Active TSS	Aorta	Aorta
36	chr6:73972200-73973400	Active TSS	Fetal Brain Female	brain
37	chr6:73972200-73973400	Active TSS	Thymus	Thymus
38	chr6:73972200-73973400	Active TSS	K562	blood
39	chr6:73972200-73973600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:73972200-73973600	Active TSS	Colon Smooth Muscle	Colon
41	chr6:73972200-73973600	Active TSS	Right Atrium	heart
42	chr6:73972200-73973600	Flanking Active TSS	HUVEC	blood vessel
43	chr6:73972200-73973800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:73972200-73973800	Active TSS	Fetal Kidney	kidney
45	chr6:73972200-73974000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:73972200-73974200	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:73972400-73973000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:73972400-73973000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:73972400-73973000	Active TSS	Primary hematopoietic stem cells	blood
50	chr6:73972400-73973000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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