Variant report

Variant	rs68004576
Chromosome Location	chr3:42632217-42632218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:352)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:352 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42631913-42632542	MCF10A-Er-Src	breast:	n/a	n/a
2	TCF12	chr3:42631993-42632575	ECC-1	luminal epithelium:	n/a	n/a
3	JUND	chr3:42631942-42632705	K562	blood:	n/a	n/a
4	EP300	chr3:42632072-42632435	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr3:42632176-42632462	GM12878	blood:	n/a	n/a
6	CHD2	chr3:42632157-42632364	HepG2	liver:	n/a	n/a
7	SIN3AK20	chr3:42632082-42632621	PANC-1	pancreas:	n/a	n/a
8	ELF1	chr3:42631931-42632627	GM12878	blood:	n/a	chr3:42632424-42632437
9	ZNF384	chr3:42631552-42632403	GM12878	blood:	n/a	n/a
10	SP1	chr3:42631939-42632537	GM12878	blood:	n/a	chr3:42632142-42632151 chr3:42632287-42632296
11	HCFC1	chr3:42631840-42632700	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr3:42631934-42632655	HepG2	liver:	n/a	n/a
13	TAF1	chr3:42632009-42632581	K562	blood:	n/a	n/a
14	POLR2A	chr3:42631938-42632671	H1-hESC	embryonic stem cell:	n/a	n/a
15	EGR1	chr3:42632153-42632328	GM12878	blood:	n/a	chr3:42632178-42632187
16	POLR2A	chr3:42631671-42632690	K562	blood:	n/a	n/a
17	MYC	chr3:42631670-42632692	NB4	blood:	n/a	n/a
18	MXI1	chr3:42631206-42633264	SK-N-SH	brain:	n/a	n/a
19	PML	chr3:42631952-42632602	K562	blood:	n/a	n/a
20	MAX	chr3:42631596-42632658	ECC-1	luminal epithelium:	n/a	n/a
21	MAFK	chr3:42632059-42632421	IMR90	lung:	n/a	n/a
22	RFX5	chr3:42631980-42632702	IMR90	lung:	n/a	n/a
23	POLR2A	chr3:42632105-42633450	IMR90	lung:	n/a	n/a
24	STAT5A	chr3:42632133-42632722	GM12878	blood:	n/a	n/a
25	EP300	chr3:42632022-42632456	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:42631595-42633611	GM12891	blood:	n/a	n/a
27	FOXP2	chr3:42632112-42632395	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr3:42631706-42633211	GM15510	blood:	n/a	n/a
29	FOS	chr3:42632069-42632446	MCF10A-Er-Src	breast:	n/a	n/a
30	GTF3C2	chr3:42632203-42633238	K562	blood:	n/a	n/a
31	POLR2A	chr3:42631764-42632768	K562	blood:	n/a	n/a
32	ELF1	chr3:42631943-42633039	GM12878	blood:	n/a	chr3:42632424-42632437
33	POLR2A	chr3:42631947-42632751	H1-neurons	neurons:	n/a	n/a
34	CHD2	chr3:42632055-42632656	Hela-S3	cervix:	n/a	n/a
35	YY1	chr3:42631667-42632450	HepG2	liver:	n/a	n/a
36	ELF1	chr3:42632076-42632870	K562	blood:	n/a	chr3:42632424-42632437
37	POU2F2	chr3:42631976-42632688	GM12891	blood:	n/a	n/a
38	ELF1	chr3:42631991-42632677	MCF-7	breast:	n/a	chr3:42632424-42632437
39	FOS	chr3:42632128-42632505	K562	blood:	n/a	n/a
40	ATF2	chr3:42631970-42632482	GM12878	blood:	n/a	n/a
41	UBTF	chr3:42632145-42632554	K562	blood:	n/a	n/a
42	FOSL2	chr3:42631995-42632452	HepG2	liver:	n/a	n/a
43	POLR2A	chr3:42631733-42632673	HUVEC	blood vessel:	n/a	n/a
44	SP1	chr3:42631993-42632452	GM12878	blood:	n/a	chr3:42632142-42632151 chr3:42632287-42632296
45	NR2F2	chr3:42631406-42632546	K562	blood:	n/a	n/a
46	HEY1	chr3:42631977-42632603	K562	blood:	n/a	n/a
47	TAF1	chr3:42631993-42632627	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:42632031-42632769	HL-60	blood:	n/a	n/a
49	MAZ	chr3:42632099-42632509	Hela-S3	cervix:	n/a	n/a
50	YY1	chr3:42631939-42632588	K562	blood:	n/a	chr3:42632510-42632521

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42631026..42632613-chr3:42695067..42697159,2	MCF-7	breast:
2	chr3:42629929..42632831-chr3:42695818..42698742,2	MCF-7	breast:
3	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
4	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
5	chr3:42630327..42632728-chr3:42670152..42672818,2	MCF-7	breast:
6	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
7	chr20:30194464..30195332-chr3:42632176..42632854,2	Hela-S3	cervix:
8	chr12:69004314..69004882-chr3:42632191..42633125,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SS18L2	TF binding region
ENSG00000127314	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000008324	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs13064597	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072295	0.82[EUR][1000 genomes]
rs13085143	1.00[ASN][1000 genomes]
rs13085695	0.82[EUR][1000 genomes]
rs13089845	0.82[EUR][1000 genomes]
rs13090902	0.82[EUR][1000 genomes]
rs13093680	0.82[EUR][1000 genomes]
rs13095447	0.82[EUR][1000 genomes]
rs13100261	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17030458	0.97[EUR][1000 genomes]
rs17074662	0.82[EUR][1000 genomes]
rs17074673	0.82[EUR][1000 genomes]
rs17074674	0.82[EUR][1000 genomes]
rs17074693	0.82[EUR][1000 genomes]
rs2284303	0.82[EUR][1000 genomes]
rs2284304	0.82[EUR][1000 genomes]
rs2300057	0.82[EUR][1000 genomes]
rs2300058	0.82[EUR][1000 genomes]
rs2302352	0.82[EUR][1000 genomes]
rs33969824	0.82[EUR][1000 genomes]
rs339705	0.89[EUR][1000 genomes]
rs33984028	0.82[EUR][1000 genomes]
rs34077739	1.00[ASN][1000 genomes]
rs34196076	1.00[ASN][1000 genomes]
rs34243788	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683820	0.82[EUR][1000 genomes]
rs34687113	0.80[EUR][1000 genomes]
rs34762478	0.82[EUR][1000 genomes]
rs34801786	0.82[EUR][1000 genomes]
rs34852409	0.82[EUR][1000 genomes]
rs34977988	0.82[EUR][1000 genomes]
rs35216140	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35676838	0.82[EUR][1000 genomes]
rs35871059	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35890296	0.82[EUR][1000 genomes]
rs36033201	0.82[EUR][1000 genomes]
rs36043081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774401	0.82[EUR][1000 genomes]
rs3774402	0.82[EUR][1000 genomes]
rs3774404	0.82[EUR][1000 genomes]
rs3774407	0.82[EUR][1000 genomes]
rs3846058	0.82[EUR][1000 genomes]
rs3846059	0.82[EUR][1000 genomes]
rs3856737	0.82[EUR][1000 genomes]
rs3900780	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[ASN][1000 genomes]
rs55994846	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56047094	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56797870	0.82[EUR][1000 genomes]
rs57259216	0.82[EUR][1000 genomes]
rs58645732	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58868911	0.82[EUR][1000 genomes]
rs59914338	0.82[EUR][1000 genomes]
rs60232916	0.82[EUR][1000 genomes]
rs60348477	0.82[EUR][1000 genomes]
rs60535002	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61149998	0.82[EUR][1000 genomes]
rs6441928	0.82[EUR][1000 genomes]
rs66786953	0.81[EUR][1000 genomes]
rs66933062	1.00[ASN][1000 genomes]
rs67059259	0.82[EUR][1000 genomes]
rs67174294	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67533173	0.80[EUR][1000 genomes]
rs67583158	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778982	0.82[EUR][1000 genomes]
rs6782164	0.82[EUR][1000 genomes]
rs67832425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788548	0.82[EUR][1000 genomes]
rs6790204	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6793186	0.82[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6795296	0.82[EUR][1000 genomes]
rs6797491	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68028490	0.82[EUR][1000 genomes]
rs68071013	0.82[EUR][1000 genomes]
rs71323162	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864022	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864072	0.82[EUR][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7616701	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617403	0.82[EUR][1000 genomes]
rs7617736	0.82[EUR][1000 genomes]
rs7623867	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7624628	0.82[EUR][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	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs68004576	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42624400-42632400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:42630800-42633000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:42631400-42632800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:42631400-42633000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:42631400-42633000	Active TSS	Osteobl	bone
6	chr3:42631600-42632800	Active TSS	Left Ventricle	heart
7	chr3:42631600-42632800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr3:42631600-42633000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:42631600-42633000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:42631600-42633000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:42631600-42633000	Active TSS	Brain Hippocampus Middle	brain
12	chr3:42631600-42633000	Active TSS	Fetal Brain Female	brain
13	chr3:42631600-42633000	Active TSS	Ovary	ovary
14	chr3:42631600-42633000	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr3:42631600-42633000	Active TSS	Small Intestine	intestine
16	chr3:42631600-42633000	Active TSS	HSMM	muscle
17	chr3:42631600-42633000	Active TSS	NH-A	brain
18	chr3:42631600-42633200	Active TSS	Aorta	Aorta
19	chr3:42631600-42633400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:42631600-42633400	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr3:42631600-42633400	Active TSS	Psoas Muscle	Psoas
22	chr3:42631600-42633400	Active TSS	HSMMtube	muscle
23	chr3:42631600-42633800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:42631800-42632400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:42631800-42632400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:42631800-42632600	Active TSS	Primary B cells from cord blood	blood
27	chr3:42631800-42632600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:42631800-42632600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:42631800-42632800	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr3:42631800-42632800	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr3:42631800-42632800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:42631800-42632800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:42631800-42632800	Active TSS	Muscle Satellite Cultured Cells	--
34	chr3:42631800-42632800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:42631800-42632800	Active TSS	Brain Angular Gyrus	brain
36	chr3:42631800-42632800	Active TSS	Colon Smooth Muscle	Colon
37	chr3:42631800-42632800	Active TSS	Esophagus	oesophagus
38	chr3:42631800-42632800	Active TSS	Fetal Muscle Leg	muscle
39	chr3:42631800-42632800	Active TSS	Placenta	Placenta
40	chr3:42631800-42632800	Active TSS	Fetal Stomach	stomach
41	chr3:42631800-42632800	Active TSS	Fetal Thymus	thymus
42	chr3:42631800-42632800	Active TSS	Lung	lung
43	chr3:42631800-42632800	Active TSS	Pancreas	Pancrea
44	chr3:42631800-42632800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr3:42631800-42632800	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:42631800-42632800	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:42631800-42632800	Active TSS	Thymus	Thymus
48	chr3:42631800-42632800	Active TSS	HUVEC	blood vessel
49	chr3:42631800-42632800	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr3:42631800-42633000	Active TSS	HUES48 Cell Line	embryonic stem cell

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