Variant report

Variant	rs11578119
Chromosome Location	chr1:170501456-170501457
allele	C/T
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	PBX3	chr1:170500675-170501855	SK-N-SH	brain:	n/a	chr1:170501260-170501269
2	EP300	chr1:170500910-170501648	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:170500639-170502010	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr1:170500794-170501759	GM12878	blood:	n/a	n/a
5	POU2F2	chr1:170501052-170501784	GM12878	blood:	n/a	n/a
6	HCFC1	chr1:170500562-170502400	Hela-S3	cervix:	n/a	n/a
7	SP1	chr1:170500628-170501797	A549	lung:	n/a	chr1:170501503-170501513 chr1:170501474-170501483 chr1:170501469-170501483 chr1:170500797-170500807
8	MAX	chr1:170500718-170501813	GM12878	blood:	n/a	n/a
9	MAX	chr1:170501392-170501683	K562	blood:	n/a	n/a
10	POLR2A	chr1:170500743-170501810	HUVEC	blood vessel:	n/a	n/a
11	IRF1	chr1:170500811-170501759	K562	blood:	n/a	chr1:170501261-170501270 chr1:170501472-170501486 chr1:170501502-170501516
12	TBP	chr1:170500694-170502321	GM12878	blood:	n/a	n/a
13	REST	chr1:170500910-170501595	A549	lung:	n/a	chr1:170500922-170500942
14	RUNX3	chr1:170500677-170501771	GM12878	blood:	n/a	n/a
15	ELF1	chr1:170500798-170501836	MCF-7	breast:	n/a	chr1:170501267-170501279 chr1:170501216-170501228
16	TAF1	chr1:170500670-170501674	MCF-7	breast:	n/a	n/a
17	ARID3A	chr1:170500705-170501967	HepG2	liver:	n/a	n/a
18	TBP	chr1:170500698-170501832	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr1:170500812-170501717	K562	blood:	n/a	n/a
20	RAD21	chr1:170501401-170501683	SK-N-SH_RA	brain:	n/a	n/a
21	BCLAF1	chr1:170500647-170501787	GM12878	blood:	n/a	chr1:170501266-170501279 chr1:170501538-170501546
22	BCL3	chr1:170500587-170501673	A549	lung:	n/a	chr1:170501266-170501279 chr1:170501538-170501546
23	GABPA	chr1:170500799-170501902	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr1:170500674-170501853	ECC-1	luminal epithelium:	n/a	n/a
25	YY1	chr1:170500801-170501802	HCT-116	colon:	n/a	chr1:170500939-170500950
26	SPI1	chr1:170500585-170501926	HL-60	blood:	n/a	n/a
27	EP300	chr1:170500603-170502035	K562	blood:	n/a	n/a
28	POU2F2	chr1:170500751-170501809	GM12891	blood:	n/a	n/a
29	MAX	chr1:170500914-170501602	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD2	chr1:170500761-170501825	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:170500687-170501865	Hela-S3	cervix:	n/a	n/a
32	ZNF143	chr1:170500749-170501836	K562	blood:	n/a	chr1:170501189-170501208
33	POLR2A	chr1:170500655-170501932	K562	blood:	n/a	n/a
34	MAX	chr1:170500676-170501534	ECC-1	luminal epithelium:	n/a	n/a
35	STAT3	chr1:170501106-170501737	MCF10A-Er-Src	breast:	n/a	chr1:170501497-170501509
36	ZNF263	chr1:170500785-170502014	HEK293-T-REx	kidney:	n/a	n/a
37	ZNF143	chr1:170500731-170501769	GM12878	blood:	n/a	chr1:170501189-170501208
38	CTBP2	chr1:170500927-170501820	H1-hESC	embryonic stem cell:	n/a	n/a
39	SMC3	chr1:170500715-170501732	GM12878	blood:	n/a	n/a
40	SP1	chr1:170500890-170501887	H1-hESC	embryonic stem cell:	n/a	chr1:170501503-170501513 chr1:170501789-170501801 chr1:170501474-170501483 chr1:170501469-170501483
41	FOXM1	chr1:170500663-170501581	GM12878	blood:	n/a	n/a
42	CHD2	chr1:170500867-170501742	K562	blood:	n/a	n/a
43	MYC	chr1:170500788-170501948	NB4	blood:	n/a	n/a
44	SMARCB1	chr1:170500749-170501965	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr1:170500773-170502777	IMR90	lung:	n/a	n/a
46	TAF1	chr1:170500538-170501804	A549	lung:	n/a	n/a
47	POLR2A	chr1:170500744-170501889	NB4	blood:	n/a	n/a
48	MAZ	chr1:170500770-170501833	K562	blood:	n/a	n/a
49	YY1	chr1:170500824-170501722	SK-N-SH_RA	brain:	n/a	chr1:170500939-170500950
50	MAFK	chr1:170500831-170501890	Hela-S3	cervix:	n/a	chr1:170501465-170501480

No.	Distal block	Cell Line	Cell type
1	chr1:170501145..170501805-chr3:33481473..33482079,2	Hela-S3	cervix:
2	chr1:169862763..169864506-chr1:170500944..170502450,2	K562	blood:
3	chr1:170499982..170502014-chr3:62799572..62801827,2	MCF-7	breast:
4	chr1:169862177..169865166-chr1:170500254..170502788,2	MCF-7	breast:
5	chr1:169862596..169865250-chr1:170499667..170504019,5	K562	blood:
6	chr1:170499494..170504219-chr1:170507198..170509728,4	K562	blood:
7	chr1:170499494..170507345-chr1:170507805..170517333,18	K562	blood:
8	chr1:170499484..170505100-chr1:170505427..170511134,13	MCF-7	breast:
9	chr1:24018042..24018553-chr1:170500938..170501655,2	Hela-S3	cervix:
10	chr1:170500034..170503040-chr1:170504550..170507151,5	K562	blood:
11	chr1:170500119..170501652-chr1:170512143..170514479,2	MCF-7	breast:
12	chr1:170499846..170504184-chr1:170513564..170517681,4	K562	blood:

Variant related genes	Relation type
ENSG00000231407	TF binding region
GORAB	TF binding region
ENSG00000142676	Chromatin interaction
ENSG00000120370	Chromatin interaction
ENSG00000153560	Chromatin interaction
ENSG00000000457	Chromatin interaction
ENSG00000252449	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10800526	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919391	1.00[ASN][1000 genomes]
rs10919403	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919405	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919406	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919408	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919410	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919416	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10919417	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919421	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919423	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919424	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919430	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1113231	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap]
rs11577004	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584810	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587811	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066718	1.00[ASN][1000 genomes]
rs12116863	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12116910	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120718	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123065	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124354	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124515	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126472	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128140	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128573	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12130086	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130520	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132914	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12134482	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12135132	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135326	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137818	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138138	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138428	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139124	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140689	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12141076	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12142689	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12145961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402306	0.89[ASN][1000 genomes]
rs12402526	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405323	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408130	0.83[AFR][1000 genomes]
rs12409985	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12724601	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333142	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412890	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537390	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591150	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350312	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1888173	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928716	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999523	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2183372	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2421326	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923079	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281371	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4399219	1.00[ASN][1000 genomes]
rs4508077	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656776	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656781	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427253	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66639118	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667728	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675683	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696114	0.83[EUR][1000 genomes]
rs6698352	0.82[ASW][hapmap];1.00[CHB][hapmap]
rs72709772	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709774	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511715	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519067	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11578119	RXRG	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170499600-170501800	Active TSS	Brain Anterior Caudate	brain
2	chr1:170499600-170502800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:170499800-170502000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:170499800-170502600	Active TSS	Aorta	Aorta
5	chr1:170500000-170501800	Active TSS	Adipose Nuclei	Adipose
6	chr1:170500000-170501800	Active TSS	Brain Angular Gyrus	brain
7	chr1:170500000-170501800	Active TSS	Brain Cingulate Gyrus	brain
8	chr1:170500000-170501800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:170500000-170502000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:170500000-170502000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:170500000-170502000	Active TSS	Brain Hippocampus Middle	brain
12	chr1:170500000-170502000	Active TSS	Duodenum Mucosa	Duodenum
13	chr1:170500000-170502000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:170500000-170502000	Active TSS	Stomach Smooth Muscle	stomach
15	chr1:170500000-170502200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:170500000-170502200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr1:170500000-170502200	Active TSS	Muscle Satellite Cultured Cells	--
18	chr1:170500000-170502200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:170500000-170502200	Active TSS	Fetal Brain Male	brain
20	chr1:170500000-170502200	Active TSS	Fetal Muscle Leg	muscle
21	chr1:170500000-170502200	Active TSS	NHEK	skin
22	chr1:170500000-170502400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:170500000-170502400	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:170500000-170502400	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr1:170500000-170502400	Active TSS	Fetal Intestine Large	intestine
26	chr1:170500000-170502400	Active TSS	HMEC	breast
27	chr1:170500000-170502400	Active TSS	K562	blood
28	chr1:170500000-170502400	Active TSS	NH-A	brain
29	chr1:170500000-170502600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:170500000-170502600	Active TSS	GM12878-XiMat	blood
31	chr1:170500000-170502800	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr1:170500000-170502800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:170500000-170503000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:170500000-170504000	Active TSS	NHLF	lung
35	chr1:170500200-170501600	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr1:170500200-170501800	Active TSS	Primary T cells from cord blood	blood
37	chr1:170500200-170501800	Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr1:170500200-170501800	Active TSS	Liver	Liver
39	chr1:170500200-170501800	Active TSS	Colon Smooth Muscle	Colon
40	chr1:170500200-170501800	Active TSS	Fetal Brain Female	brain
41	chr1:170500200-170501800	Active TSS	Spleen	Spleen
42	chr1:170500200-170501800	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr1:170500200-170502000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:170500200-170502000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:170500200-170502000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:170500200-170502000	Active TSS	Brain Substantia Nigra	brain
47	chr1:170500200-170502000	Active TSS	Esophagus	oesophagus
48	chr1:170500200-170502000	Active TSS	Left Ventricle	heart
49	chr1:170500200-170502000	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:170500200-170502000	Active TSS	Thymus	Thymus

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