Variant report

Variant	rs2531804
Chromosome Location	chr6:28411303-28411304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:203)
CpG islands
(count:244)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:203 , 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	TAF1	chr6:28410976-28411481	PFSK-1	brain:	n/a	n/a
2	GATA2	chr6:28410980-28411419	SH-SY5Y	brain:	n/a	n/a
3	SIN3AK20	chr6:28410881-28411499	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr6:28410952-28411426	ECC-1	luminal epithelium:	n/a	n/a
5	GABPA	chr6:28410914-28411619	HL-60	blood:	n/a	n/a
6	POLR2A	chr6:28410994-28411537	HEK293	kidney:	n/a	n/a
7	ZNF143	chr6:28411240-28411374	K562	blood:	n/a	n/a
8	POU2F2	chr6:28411055-28411309	GM12878	blood:	n/a	n/a
9	POU2F2	chr6:28410979-28411457	GM12891	blood:	n/a	n/a
10	POLR2A	chr6:28411044-28411432	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr6:28411027-28411375	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:28410968-28411532	GM18526	blood:	n/a	n/a
13	POLR2A	chr6:28410868-28411530	U87	brain:	n/a	n/a
14	CTCF	chr6:28411160-28411310	RPTEC	kidney:	n/a	n/a
15	REST	chr6:28410108-28411838	H1-neurons	neurons:	n/a	chr6:28411290-28411310
16	POLR2A	chr6:28410742-28411563	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:28410935-28411427	GM12892	blood:	n/a	n/a
18	POLR2A	chr6:28411043-28411379	K562	blood:	n/a	n/a
19	POLR2A	chr6:28410995-28411577	GM12891	blood:	n/a	n/a
20	BACH1	chr6:28411264-28411539	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:28410990-28411525	GM12892	blood:	n/a	n/a
22	NRF1	chr6:28411164-28411375	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:28410952-28411592	HL-60	blood:	n/a	n/a
24	CTCF	chr6:28411239-28411313	Spleen_OC	spleen:	n/a	n/a
25	GABPA	chr6:28410826-28411712	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr6:28410986-28411472	GM15510	blood:	n/a	n/a
27	SP2	chr6:28411133-28411421	K562	blood:	n/a	n/a
28	BCLAF1	chr6:28410933-28411596	GM12878	blood:	n/a	n/a
29	EP300	chr6:28410989-28411485	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr6:28411166-28411514	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:28410978-28411550	GM19099	blood:	n/a	n/a
32	FOS	chr6:28411127-28411479	HUVEC	blood vessel:	n/a	n/a
33	HEY1	chr6:28411049-28411440	HepG2	liver:	n/a	n/a
34	ZEB1	chr6:28410898-28411393	GM12878	blood:	n/a	n/a
35	CREB1	chr6:28410967-28411492	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:28410795-28411679	H1-neurons	neurons:	n/a	n/a
37	RELA	chr6:28411048-28411482	GM15510	blood:	n/a	n/a
38	POLR2A	chr6:28410963-28411463	Gliobla	brain:	n/a	n/a
39	POLR2A	chr6:28410902-28411421	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr6:28411200-28411350	HCPEpiC	choroid plexus:	n/a	n/a
41	POLR2A	chr6:28410819-28411530	U87	brain:	n/a	n/a
42	POLR2A	chr6:28411020-28411546	SK-N-SH	brain:	n/a	n/a
43	TCF12	chr6:28411134-28411407	GM12878	blood:	n/a	n/a
44	POLR2A	chr6:28410642-28411556	MCF10A-Er-Src	breast:	n/a	n/a
45	TAF1	chr6:28411057-28411348	GM12891	blood:	n/a	n/a
46	RCOR1	chr6:28411043-28411618	GM12878	blood:	n/a	n/a
47	EGR1	chr6:28411089-28411511	H1-hESC	embryonic stem cell:	n/a	n/a
48	STAT3	chr6:28411171-28411464	MCF10A-Er-Src	breast:	n/a	chr6:28411325-28411336
49	TAF1	chr6:28410739-28411489	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr6:28411078-28411402	K562	blood:	n/a	n/a

(count:244 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28411279-28411329	LNCaP	prostate:	n/a
2	chr6:28411271-28411321	Hela-S3	cervix:	n/a
3	chr6:28411271-28411321	HNPCEpiC	eye:	n/a
4	chr6:28411271-28411321	MCF10A-Er-Src	breast:	n/a
5	chr6:28411285-28411335	GM19239	blood:	n/a
6	chr6:28411279-28411329	PFSK-1	brain:	n/a
7	chr6:28411285-28411335	AG04449	skin:	fetal
8	chr6:28411279-28411329	U87	brain:	n/a
9	chr6:28411271-28411321	H1-hESC	embryonic stem cell:	embryo
10	chr6:28411279-28411329	HAEpiC	amniotic membrane:	n/a
11	chr6:28411279-28411329	H1-hESC	embryonic stem cell:	embryo
12	chr6:28411271-28411321	HL-60	blood:	n/a
13	chr6:28411287-28411337	AG04449	skin:	fetal
14	chr6:28411287-28411337	T-47D	breast:	n/a
15	chr6:28411287-28411337	GM12892	blood:	n/a
16	chr6:28411287-28411337	PrEC	prostate:	n/a
17	chr6:28411287-28411337	NT2-D1	testis:	n/a
18	chr6:28411287-28411337	NH-A	brain:	n/a
19	chr6:28411279-28411329	GM12891	blood:	n/a
20	chr6:28411285-28411335	AG09309	skin:	n/a
21	chr6:28411287-28411337	HPAEpiC	pulmonary alveolar:	n/a
22	chr6:28411271-28411321	GM12892	blood:	n/a
23	chr6:28411279-28411329	GM06990	blood:	n/a
24	chr6:28411285-28411335	NB4	blood:	n/a
25	chr6:28411279-28411329	GM19239	blood:	n/a
26	chr6:28411287-28411337	K562	blood:	n/a
27	chr6:28411279-28411329	HUVEC	blood vessel:	n/a
28	chr6:28411279-28411329	AG09309	skin:	n/a
29	chr6:28411285-28411335	Caco-2	colon:	n/a
30	chr6:28411285-28411335	HEEpiC	esophagus:	n/a
31	chr6:28411271-28411321	HCPEpiC	choroid plexus:	n/a
32	chr6:28411287-28411337	Jurkat	blood:	n/a
33	chr6:28411287-28411337	SK-N-SH_RA	brain:	n/a
34	chr6:28411285-28411335	HepG2	liver:	n/a
35	chr6:28411271-28411321	NB4	blood:	n/a
36	chr6:28411271-28411321	HEEpiC	esophagus:	n/a
37	chr6:28411279-28411329	Hepatocyte	liver:	n/a
38	chr6:28411287-28411337	HRCEpiC	kidney:	n/a
39	chr6:28411271-28411321	SKMC	muscle:	n/a
40	chr6:28411271-28411321	IMR90	lung:	fetal
41	chr6:28411285-28411335	HPAEpiC	pulmonary alveolar:	n/a
42	chr6:28411285-28411335	AG04450	lung:	fetal
43	chr6:28411285-28411335	SK-N-SH_RA	brain:	n/a
44	chr6:28411287-28411337	HRPEpiC	eye:	n/a
45	chr6:28411287-28411337	HRE	kidney:	n/a
46	chr6:28411285-28411335	ovcar-3	ovarian:	n/a
47	chr6:28411285-28411335	IMR90	lung:	fetal
48	chr6:28411279-28411329	ECC-1	luminal epithelium:	n/a
49	chr6:28411287-28411337	SKMC	muscle:	n/a
50	chr6:28411285-28411335	T-47D	breast:	n/a

No data

Variant related genes	Relation type
ZSCAN23	TF binding region
COX11P1	TF binding region
COX11P1	CpG island
ZSCAN23	CpG island

Extended variants
information (count: 80 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1005127	0.85[ASN][1000 genomes]
rs1054372	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1124131	0.87[ASN][1000 genomes]
rs11751693	0.84[ASN][1000 genomes]
rs11752496	0.82[ASN][1000 genomes]
rs11752919	0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11754208	0.85[ASN][1000 genomes]
rs11755942	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11760133	0.87[ASN][1000 genomes]
rs12697938	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13201726	0.88[ASN][1000 genomes]
rs13201753	0.87[JPT][hapmap]
rs13207208	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13210866	0.87[ASN][1000 genomes]
rs13215476	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1339898	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13437294	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1361385	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1416918	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1558205	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1591913	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16894021	0.84[ASN][1000 genomes]
rs16894060	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs16894095	0.90[ASN][1000 genomes]
rs16894108	0.88[ASN][1000 genomes]
rs2027361	0.90[ASN][1000 genomes]
rs2041230	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2071965	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs213228	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs2531803	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs28360638	0.85[ASN][1000 genomes]
rs34513104	0.85[ASN][1000 genomes]
rs35191424	0.85[ASN][1000 genomes]
rs35560946	0.90[ASN][1000 genomes]
rs35599905	0.86[ASN][1000 genomes]
rs36018474	0.88[ASN][1000 genomes]
rs3734563	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3800328	0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4254981	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4357130	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4580862	0.85[ASN][1000 genomes]
rs4642462	0.90[ASN][1000 genomes]
rs66542396	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67211468	0.88[ASN][1000 genomes]
rs6899389	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6899603	0.85[ASN][1000 genomes]
rs6903535	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6907950	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6908137	0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6917130	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6922169	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6922374	1.00[JPT][hapmap]
rs6922429	0.87[ASN][1000 genomes]
rs6927229	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6928773	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6929825	0.83[ASN][1000 genomes]
rs6939966	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs740621	0.90[ASN][1000 genomes]
rs740622	0.90[ASN][1000 genomes]
rs7740351	0.90[ASN][1000 genomes]
rs7749736	0.85[ASN][1000 genomes]
rs7759191	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7764722	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7764737	0.85[ASN][1000 genomes]
rs7773051	0.85[ASN][1000 genomes]
rs7775132	0.85[ASN][1000 genomes]
rs916403	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs9461456	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9461458	0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9461459	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9468354	0.85[ASN][1000 genomes]
rs9468355	0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9468357	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9468360	0.84[ASN][1000 genomes]
rs9468361	0.85[ASN][1000 genomes]
rs9468365	0.85[ASN][1000 genomes]
rs9468366	0.84[ASN][1000 genomes]
rs9468367	0.85[ASN][1000 genomes]
rs9468368	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9468370	0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2531804	ZSCAN23	cis	Artery Tibial	GTEx
rs2531804	HIST1H2BO	cis	parietal	SCAN
rs2531804	HIST1H2BN	cis	cerebellum	SCAN
rs2531804	ZSCAN23	cis	parietal	SCAN
rs2531804	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs2531804	ZNF192	cis	cerebellum	SCAN
rs2531804	ZSCAN31	cis	lung	GTEx
rs2531804	ZNF323	cis	parietal	SCAN
rs2531804	ZSCAN23	cis	cerebellum	SCAN
rs2531804	ZNF187	cis	cerebellum	SCAN
rs2531804	AL022393.7	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28410000-28411800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr6:28410000-28411800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr6:28410200-28411600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28410200-28411600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:28410200-28411600	Active TSS	Brain Anterior Caudate	brain
6	chr6:28410200-28411600	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr6:28410200-28411600	Active TSS	NHLF	lung
8	chr6:28410200-28411800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr6:28410200-28411800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:28410200-28411800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:28410200-28411800	Active TSS	Brain Angular Gyrus	brain
12	chr6:28410200-28411800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:28410200-28412000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:28410200-28412000	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:28410200-28412000	Flanking Active TSS	Dnd41	blood
16	chr6:28410400-28411400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:28410400-28411400	Active TSS	Fetal Intestine Small	intestine
18	chr6:28410400-28411600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr6:28410400-28411600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:28410400-28411600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:28410400-28411600	Active TSS	Brain Substantia Nigra	brain
22	chr6:28410400-28411600	Active TSS	GM12878-XiMat	blood
23	chr6:28410400-28411800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:28410400-28411800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:28410400-28411800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:28410400-28411800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:28410400-28411800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr6:28410400-28411800	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr6:28410400-28411800	Active TSS	Fetal Brain Female	brain
30	chr6:28410400-28411800	Active TSS	Fetal Lung	lung
31	chr6:28410400-28411800	Active TSS	Right Atrium	heart
32	chr6:28410400-28411800	Active TSS	NHEK	skin
33	chr6:28410400-28412000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr6:28410400-28412000	Active TSS	Psoas Muscle	Psoas
35	chr6:28410400-28412400	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr6:28410600-28411400	Active TSS	Colon Smooth Muscle	Colon
37	chr6:28410600-28411400	Active TSS	Fetal Intestine Large	intestine
38	chr6:28410600-28411600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:28410600-28411600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:28410600-28411600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:28410600-28411600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:28410600-28411600	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:28410600-28411600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr6:28410600-28411600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr6:28410600-28411600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr6:28410600-28411600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:28410600-28411600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:28410600-28411600	Active TSS	Aorta	Aorta
49	chr6:28410600-28411600	Active TSS	Brain Germinal Matrix	brain
50	chr6:28410600-28411600	Active TSS	Fetal Muscle Leg	muscle

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