Variant report

Variant	rs967116
Chromosome Location	chr8:50824431-50824432
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	REST	chr8:50822049-50824821	PFSK-1	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269 chr8:50822601-50822614
2	TEAD4	chr8:50824136-50824507	H1-hESC	embryonic stem cell:	n/a	n/a
3	REST	chr8:50823829-50824541	PANC-1	pancreas:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
4	POLR2A	chr8:50824148-50824464	MCF-7	breast:	n/a	n/a
5	CTCF	chr8:50824187-50824431	MCF-7	breast:	n/a	n/a
6	MYC	chr8:50824162-50824492	MCF-7	breast:	n/a	n/a
7	REST	chr8:50824092-50824433	HepG2	liver:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
8	REST	chr8:50824121-50824485	U87	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
9	REST	chr8:50824134-50824480	SK-N-SH	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
10	REST	chr8:50823774-50824665	PANC-1	pancreas:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
11	FOXP2	chr8:50824146-50824440	PFSK-1	brain:	n/a	n/a
12	REST	chr8:50823982-50824581	ECC-1	luminal epithelium:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
13	REST	chr8:50823868-50824734	PFSK-1	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
14	REST	chr8:50823806-50824635	U87	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
15	TBP	chr8:50824129-50824448	H1-hESC	embryonic stem cell:	n/a	n/a
16	JUND	chr8:50824036-50824488	H1-hESC	embryonic stem cell:	n/a	n/a
17	REST	chr8:50823826-50824619	HepG2	liver:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
18	MAX	chr8:50824077-50824464	MCF-7	breast:	n/a	n/a
19	REST	chr8:50824117-50824446	GM12878	blood:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
20	REST	chr8:50823682-50824756	PANC-1	pancreas:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
21	RAD21	chr8:50824033-50824516	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr8:50822051-50824817	PFSK-1	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269 chr8:50822601-50822614
23	REST	chr8:50824034-50824452	K562	blood:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
24	REST	chr8:50824088-50824491	HepG2	liver:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
25	RCOR1	chr8:50824162-50824444	HepG2	liver:	n/a	n/a
26	REST	chr8:50824075-50824482	PANC-1	pancreas:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
27	SIN3AK20	chr8:50824136-50824436	H1-hESC	embryonic stem cell:	n/a	n/a
28	HDAC2	chr8:50824103-50824515	MCF-7	breast:	n/a	n/a
29	HDAC2	chr8:50824066-50824508	MCF-7	breast:	n/a	n/a
30	REST	chr8:50822077-50824754	H1-neurons	neurons:	n/a	chr8:50824275-50824282 chr8:50824255-50824269 chr8:50822601-50822614
31	CHD2	chr8:50824143-50824446	H1-hESC	embryonic stem cell:	n/a	n/a
32	REST	chr8:50823713-50824772	MCF-7	breast:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
33	REST	chr8:50823842-50824624	H1-hESC	embryonic stem cell:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
34	POLR2A	chr8:50822917-50824527	H1-neurons	neurons:	n/a	n/a
35	REST	chr8:50823977-50824551	HL-60	blood:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
36	MAX	chr8:50824153-50824434	H1-hESC	embryonic stem cell:	n/a	n/a
37	TEAD4	chr8:50824041-50824608	A549	lung:	n/a	n/a
38	REST	chr8:50823539-50824779	HL-60	blood:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
39	REST	chr8:50823832-50824513	HepG2	liver:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
40	CTBP2	chr8:50823956-50824543	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr8:50824141-50824547	MCF-7	breast:	n/a	n/a
42	MYC	chr8:50824192-50824440	MCF-7	breast:	n/a	n/a
43	REST	chr8:50823786-50824702	SK-N-SH	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
44	REST	chr8:50824074-50824516	PFSK-1	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
45	REST	chr8:50823780-50824632	ECC-1	luminal epithelium:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
46	REST	chr8:50824090-50824479	Hela-S3	cervix:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
47	REST	chr8:50824088-50824446	PANC-1	pancreas:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
48	REST	chr8:50823806-50824633	U87	brain:	n/a	chr8:50824275-50824282 chr8:50824255-50824269
49	RCOR1	chr8:50824254-50824434	K562	blood:	n/a	n/a
50	REST	chr8:50824149-50824511	HCT-116	colon:	n/a	chr8:50824275-50824282 chr8:50824255-50824269

Variant related genes	Relation type
SNTG1	TF binding region
ENSG00000271148	TF binding region

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10086004	0.81[EUR][1000 genomes]
rs10089399	0.81[EUR][1000 genomes]
rs10090657	0.81[EUR][1000 genomes]
rs10092384	0.81[EUR][1000 genomes]
rs10504092	0.84[EUR][1000 genomes]
rs1074385	0.82[EUR][1000 genomes]
rs11785147	0.81[EUR][1000 genomes]
rs12542041	0.81[EUR][1000 genomes]
rs13251355	0.82[EUR][1000 genomes]
rs13267366	0.81[CEU][hapmap]
rs1352112	0.81[EUR][1000 genomes]
rs1352117	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs1385311	0.89[CEU][hapmap]
rs1385974	0.81[EUR][1000 genomes]
rs1385975	0.81[EUR][1000 genomes]
rs1385976	0.80[EUR][1000 genomes]
rs1484807	1.00[MEX][hapmap]
rs1486241	0.81[EUR][1000 genomes]
rs1486242	0.81[EUR][1000 genomes]
rs1486243	0.81[EUR][1000 genomes]
rs1486245	0.83[EUR][1000 genomes]
rs1486251	0.81[EUR][1000 genomes]
rs1486252	0.81[EUR][1000 genomes]
rs1486258	0.82[TSI][hapmap]
rs1552372	0.81[EUR][1000 genomes]
rs1580468	0.82[EUR][1000 genomes]
rs167629	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs167630	0.89[CEU][hapmap]
rs172758	1.00[YRI][hapmap]
rs17674389	0.90[CEU][hapmap]
rs17674783	0.84[EUR][1000 genomes]
rs17747294	0.84[EUR][1000 genomes]
rs17747567	0.84[EUR][1000 genomes]
rs17747896	0.84[EUR][1000 genomes]
rs17747929	0.84[EUR][1000 genomes]
rs182646	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2129162	0.82[EUR][1000 genomes]
rs2129165	0.82[EUR][1000 genomes]
rs2170953	0.85[TSI][hapmap]
rs2200494	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs223081	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2385544	0.84[EUR][1000 genomes]
rs2385545	0.81[EUR][1000 genomes]
rs2385546	0.82[EUR][1000 genomes]
rs2385547	0.82[EUR][1000 genomes]
rs2385548	0.82[EUR][1000 genomes]
rs2385554	0.85[TSI][hapmap]
rs2449957	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2449958	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2449959	0.83[EUR][1000 genomes]
rs2450285	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2450288	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2450291	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2628417	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2630550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs318860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs318862	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs318864	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs318870	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318871	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318872	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318873	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318875	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318877	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs318884	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318885	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318888	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318890	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318893	0.89[CEU][hapmap];1.00[YRI][hapmap]
rs318894	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs318902	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs318903	0.89[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs318905	0.89[CEU][hapmap];0.87[YRI][hapmap]
rs318906	0.89[CEU][hapmap]
rs318908	0.89[CEU][hapmap]
rs318910	0.89[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap]
rs318911	0.89[CEU][hapmap]
rs318912	0.89[CEU][hapmap]
rs365318	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs366526	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs380279	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs384406	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs391798	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs402156	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs406337	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs415276	0.90[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs417918	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs436688	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4377975	0.85[EUR][1000 genomes]
rs4383988	0.81[EUR][1000 genomes]
rs4584153	0.81[EUR][1000 genomes]
rs55920504	0.85[EUR][1000 genomes]
rs57585353	0.84[EUR][1000 genomes]
rs58597929	0.85[EUR][1000 genomes]
rs59405147	0.83[EUR][1000 genomes]
rs60061614	0.84[EUR][1000 genomes]
rs6472722	1.00[CEU][hapmap]
rs7008924	0.81[EUR][1000 genomes]
rs7013903	0.81[EUR][1000 genomes]
rs72638307	0.84[EUR][1000 genomes]
rs72638311	0.84[EUR][1000 genomes]
rs72638312	0.84[EUR][1000 genomes]
rs72638332	0.84[EUR][1000 genomes]
rs72638338	0.85[EUR][1000 genomes]
rs7825552	0.81[EUR][1000 genomes]
rs9298228	0.81[EUR][1000 genomes]
rs9298229	0.81[EUR][1000 genomes]
rs964011	0.81[EUR][1000 genomes]
rs967109	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs967110	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9886451	0.81[EUR][1000 genomes]
rs993552	0.89[CEU][hapmap]

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	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs967116	SNTG1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50821400-50824600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:50821400-50825000	Active TSS	Fetal Brain Female	brain
3	chr8:50821400-50826800	Active TSS	Fetal Brain Male	brain
4	chr8:50821600-50824600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr8:50821600-50824600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr8:50821600-50829000	Active TSS	Brain Germinal Matrix	brain
7	chr8:50821800-50824800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
8	chr8:50821800-50825200	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr8:50821800-50827800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr8:50821800-50828600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr8:50822000-50824600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr8:50822000-50824600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr8:50822000-50828400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:50822200-50824600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr8:50822600-50824600	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr8:50823400-50826800	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr8:50823400-50828400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:50823600-50824600	Enhancers	Liver	Liver
19	chr8:50823600-50825600	Active TSS	Brain Angular Gyrus	brain
20	chr8:50823800-50824600	Bivalent Enhancer	Fetal Lung	lung
21	chr8:50824000-50824600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:50824000-50824600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr8:50824000-50824600	Bivalent Enhancer	HMEC	breast
24	chr8:50824000-50826000	Active TSS	Brain Cingulate Gyrus	brain
25	chr8:50824000-50828600	Active TSS	Brain Anterior Caudate	brain
26	chr8:50824200-50824600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:50824200-50824600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr8:50824200-50824600	Bivalent Enhancer	Fetal Intestine Small	intestine
29	chr8:50824400-50824600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr8:50824400-50824600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr8:50824400-50824600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr8:50824400-50824600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr8:50824400-50824600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr8:50824400-50824600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
35	chr8:50824400-50824600	Bivalent Enhancer	Fetal Intestine Large	intestine
36	chr8:50824400-50824600	Bivalent Enhancer	Fetal Stomach	stomach
37	chr8:50824400-50824800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:50824400-50824800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
39	chr8:50824400-50824800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
40	chr8:50824400-50824800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr8:50824400-50825000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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