Variant report

Variant	rs3808609
Chromosome Location	chr8:59465377-59465378
allele	C/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	EBF1	chr8:59465276-59466007	GM12878	blood:	n/a	chr8:59465418-59465429
2	BHLHE40	chr8:59465310-59466031	K562	blood:	n/a	n/a
3	ZBTB7A	chr8:59465169-59466301	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr8:59465303-59466610	Raji	blood:	n/a	n/a
5	PAX5	chr8:59465306-59466081	GM12878	blood:	n/a	n/a
6	MAX	chr8:59465330-59466063	SK-N-SH	brain:	n/a	n/a
7	EP300	chr8:59465312-59466054	GM12878	blood:	n/a	chr8:59465519-59465528 chr8:59465831-59465847 chr8:59465832-59465841 chr8:59465898-59465914
8	SIN3AK20	chr8:59465350-59465650	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr8:59465352-59466735	GM12891	blood:	n/a	n/a
10	POLR2A	chr8:59465259-59466646	SK-N-MC	brain:	n/a	n/a
11	STAT5A	chr8:59465162-59465790	GM12878	blood:	n/a	n/a
12	MAX	chr8:59465327-59466630	K562	blood:	n/a	n/a
13	SIN3AK20	chr8:59465354-59466816	MCF-7	breast:	n/a	n/a
14	EGR1	chr8:59465240-59466286	HCT-116	colon:	n/a	chr8:59465732-59465747 chr8:59465734-59465745 chr8:59465504-59465517 chr8:59465733-59465746 chr8:59465733-59465746 chr8:59465827-59465837 chr8:59465736-59465745 chr8:59466184-59466197 chr8:59465503-59465518 chr8:59465733-59465746 chr8:59465505-59465516 chr8:59465733-59465747
15	PAX5	chr8:59465348-59466002	GM12892	blood:	n/a	n/a
16	MAZ	chr8:59465356-59466712	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr8:59465300-59465450	HCPEpiC	choroid plexus:	n/a	n/a
18	CREB1	chr8:59465369-59466152	A549	lung:	n/a	n/a
19	POLR2A	chr8:59465362-59466303	MCF-7	breast:	n/a	n/a
20	POLR2A	chr8:59464953-59467986	PBDE	blood:	n/a	n/a
21	POLR2A	chr8:59465376-59466465	K562	blood:	n/a	n/a
22	SIN3A	chr8:59465204-59466748	H1-hESC	embryonic stem cell:	n/a	chr8:59465628-59465637
23	EGR1	chr8:59465288-59465983	K562	blood:	n/a	chr8:59465732-59465747 chr8:59465734-59465745 chr8:59465504-59465517 chr8:59465733-59465746 chr8:59465733-59465746 chr8:59465827-59465837 chr8:59465736-59465745 chr8:59465503-59465518 chr8:59465733-59465746 chr8:59465505-59465516 chr8:59465733-59465747
24	POLR2A	chr8:59465264-59466077	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr8:59465295-59466161	A549	lung:	n/a	n/a
26	HMGN3	chr8:59465316-59466373	K562	blood:	n/a	n/a
27	ZNF143	chr8:59465369-59465892	K562	blood:	n/a	n/a
28	POLR2A	chr8:59465342-59466235	H1-neurons	neurons:	n/a	n/a
29	CHD2	chr8:59465330-59466690	K562	blood:	n/a	chr8:59466017-59466027
30	POLR2A	chr8:59465315-59466345	Gliobla	brain:	n/a	n/a
31	PML	chr8:59465340-59466724	K562	blood:	n/a	chr8:59466534-59466543
32	REST	chr8:59465001-59466928	H1-neurons	neurons:	n/a	n/a
33	TBL1XR1	chr8:59465276-59466002	GM12878	blood:	n/a	n/a
34	TAF1	chr8:59465143-59466103	H1-hESC	embryonic stem cell:	n/a	n/a
35	FOXP2	chr8:59465377-59466144	PFSK-1	brain:	n/a	n/a
36	ZNF143	chr8:59465263-59466026	GM12878	blood:	n/a	chr8:59465905-59465915 chr8:59465907-59465925
37	CREB1	chr8:59465337-59466178	H1-hESC	embryonic stem cell:	n/a	n/a
38	RUNX3	chr8:59465348-59466048	GM12878	blood:	n/a	n/a
39	POLR2A	chr8:59465163-59466449	H1-neurons	neurons:	n/a	n/a
40	HA-E2F1	chr8:59465322-59466041	MCF-7	breast:	n/a	chr8:59465831-59465841
41	ZBTB7A	chr8:59465297-59466316	K562	blood:	n/a	n/a
42	GATA1	chr8:59465036-59467267	PBDE	blood:	n/a	n/a
43	POLR2A	chr8:59465310-59466392	HepG2	liver:	n/a	n/a
44	EGR1	chr8:59465222-59466130	HCT-116	colon:	n/a	chr8:59465732-59465747 chr8:59465734-59465745 chr8:59465504-59465517 chr8:59465733-59465746 chr8:59465733-59465746 chr8:59465827-59465837 chr8:59465736-59465745 chr8:59465503-59465518 chr8:59465733-59465746 chr8:59465505-59465516 chr8:59465733-59465747
45	ZMIZ1	chr8:59465269-59466067	K562	blood:	n/a	n/a
46	E2F4	chr8:59465237-59465950	MCF10A-Er-Src	breast:	n/a	chr8:59465831-59465841
47	EGR1	chr8:59465270-59465999	MCF-7	breast:	n/a	chr8:59465732-59465747 chr8:59465734-59465745 chr8:59465504-59465517 chr8:59465733-59465746 chr8:59465733-59465746 chr8:59465827-59465837 chr8:59465736-59465745 chr8:59465503-59465518 chr8:59465733-59465746 chr8:59465505-59465516 chr8:59465733-59465747
48	POLR2A	chr8:59465350-59466877	IMR90	lung:	n/a	n/a
49	POLR2A	chr8:59465360-59466122	SK-N-SH	brain:	n/a	n/a
50	EBF1	chr8:59465348-59466056	GM12878	blood:	n/a	chr8:59465418-59465429

No.	Distal block	Cell Line	Cell type
1	chr8:59464567..59467546-chr8:59474944..59480287,7	MCF-7	breast:
2	chr8:59464966..59467045-chr8:59571709..59574474,2	MCF-7	breast:
3	chr8:59465084..59467484-chr8:59482976..59485277,2	MCF-7	breast:
4	chr8:59465077..59468758-chr8:59483246..59485751,3	MCF-7	breast:
5	chr7:35839732..35840580-chr8:59465212..59466200,2	Hela-S3	cervix:
6	chr8:59464841..59467426-chr8:59569762..59573398,4	MCF-7	breast:
7	chr8:59463736..59468207-chr8:59482369..59488045,4	K562	blood:
8	chr8:59464704..59467459-chr8:59489336..59490887,2	MCF-7	breast:
9	chr8:59464523..59466345-chr8:59503286..59506269,2	K562	blood:

Variant related genes	Relation type
SDCBP	TF binding region
ENSG00000035681	Chromatin interaction
ENSG00000228878	Chromatin interaction
ENSG00000122545	Chromatin interaction
ENSG00000137575	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10085973	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs10090425	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10090964	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10092359	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10094910	0.83[EUR][1000 genomes]
rs10099153	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10099240	0.83[EUR][1000 genomes]
rs10099912	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10100873	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10102709	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10104292	0.82[CEU][hapmap]
rs10106272	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10107530	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10110065	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10110111	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10111052	0.83[EUR][1000 genomes]
rs10111506	0.94[EUR][1000 genomes]
rs10113750	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10504256	0.83[CEU][hapmap]
rs1050488	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1050504	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11774558	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11775194	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11776003	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11782455	0.83[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11783174	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11785141	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12335008	0.91[EUR][1000 genomes]
rs12674568	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12676593	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12677290	0.82[CEU][hapmap]
rs12678669	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12680104	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12680996	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs16923562	0.94[EUR][1000 genomes]
rs16923564	0.94[EUR][1000 genomes]
rs17263989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1976162	0.83[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1991359	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2279460	0.82[CEU][hapmap]
rs2279462	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs28429491	0.94[EUR][1000 genomes]
rs28650441	0.94[EUR][1000 genomes]
rs28656336	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28711402	0.82[AMR][1000 genomes]
rs28809811	0.80[EUR][1000 genomes]
rs3739327	0.82[EUR][1000 genomes]
rs3816846	0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4282557	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4400367	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs4579515	0.82[CEU][hapmap]
rs55774738	0.94[EUR][1000 genomes]
rs56249776	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59979442	0.90[EUR][1000 genomes]
rs6471729	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6471731	0.84[EUR][1000 genomes]
rs6981601	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6986129	0.94[EUR][1000 genomes]
rs6995115	0.83[CEU][hapmap]
rs7009248	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7009374	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7011095	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7014398	0.94[EUR][1000 genomes]
rs72647424	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72647425	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72647434	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72647435	0.91[EUR][1000 genomes]
rs72647437	0.85[AMR][1000 genomes]
rs72647443	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7817515	0.93[EUR][1000 genomes]
rs7825996	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs7826122	0.83[CEU][hapmap]
rs7827910	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7843989	0.85[EUR][1000 genomes]
rs7844231	0.83[CEU][hapmap]
rs9297995	0.93[EUR][1000 genomes]
rs9297997	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs9297998	0.82[CEU][hapmap]
rs9297999	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59464600-59468200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr8:59464800-59465400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr8:59464800-59467200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr8:59464800-59468600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:59465000-59465400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
6	chr8:59465000-59465400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr8:59465000-59465400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:59465000-59465400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr8:59465000-59465400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr8:59465000-59465400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr8:59465000-59465400	Flanking Active TSS	Liver	Liver
12	chr8:59465000-59465400	Active TSS	Brain Germinal Matrix	brain
13	chr8:59465000-59465400	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr8:59465000-59465400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr8:59465000-59465400	Flanking Active TSS	Fetal Heart	heart
16	chr8:59465000-59465400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
17	chr8:59465000-59465400	Active TSS	Fetal Muscle Trunk	muscle
18	chr8:59465000-59465400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr8:59465000-59465400	Flanking Active TSS	A549	lung
20	chr8:59465000-59465400	Flanking Active TSS	HUVEC	blood vessel
21	chr8:59465000-59465400	Flanking Active TSS	NHEK	skin
22	chr8:59465000-59465400	Flanking Active TSS	Osteobl	bone
23	chr8:59465000-59465600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr8:59465000-59465600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr8:59465000-59465600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr8:59465000-59465600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr8:59465000-59465600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr8:59465000-59465600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr8:59465000-59465600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr8:59465000-59465600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:59465000-59465600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr8:59465000-59465600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr8:59465000-59465600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr8:59465000-59465600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr8:59465000-59465600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr8:59465000-59465600	Flanking Bivalent TSS/Enh	Dnd41	blood
37	chr8:59465000-59467000	Active TSS	H1 Cell Line	embryonic stem cell
38	chr8:59465000-59467000	Active TSS	H9 Cell Line	embryonic stem cell
39	chr8:59465000-59467000	Active TSS	Primary T cells from cord blood	blood
40	chr8:59465000-59467000	Active TSS	Brain Cingulate Gyrus	brain
41	chr8:59465000-59467000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr8:59465000-59467000	Active TSS	Brain Substantia Nigra	brain
43	chr8:59465000-59467000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr8:59465000-59467200	Active TSS	Brain Angular Gyrus	brain
45	chr8:59465000-59467200	Active TSS	Fetal Lung	lung
46	chr8:59465000-59467200	Active TSS	Fetal Stomach	stomach
47	chr8:59465000-59467200	Active TSS	NH-A	brain
48	chr8:59465000-59467400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr8:59465000-59467400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr8:59465000-59467400	Active TSS	Rectal Smooth Muscle	rectum

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