Variant report

Variant	rs6692116
Chromosome Location	chr1:210111242-210111243
allele	A/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	chr1:210110760-210111306	PFSK-1	brain:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
2	POLR2A	chr1:210111091-210111324	HUVEC	blood vessel:	n/a	n/a
3	MYC	chr1:210110965-210111279	MCF10A-Er-Src	breast:	n/a	n/a
4	SIN3AK20	chr1:210110720-210111325	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOS	chr1:210111042-210111246	MCF10A-Er-Src	breast:	n/a	n/a
6	REST	chr1:210110852-210111427	PANC-1	pancreas:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
7	FOXP2	chr1:210111088-210111269	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr1:210110641-210112159	H1-neurons	neurons:	n/a	n/a
9	REST	chr1:210110668-210111510	K562	blood:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
10	MAX	chr1:210111000-210111372	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr1:210111148-210112212	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr1:210110964-210111324	HepG2	liver:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
13	REST	chr1:210110703-210111322	A549	lung:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
14	REST	chr1:210110747-210111323	Hela-S3	cervix:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
15	BACH1	chr1:210110958-210111334	H1-hESC	embryonic stem cell:	n/a	n/a
16	RCOR1	chr1:210110998-210111283	HepG2	liver:	n/a	n/a
17	REST	chr1:210110712-210111317	Hela-S3	cervix:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
18	RCOR1	chr1:210110976-210111322	K562	blood:	n/a	n/a
19	REST	chr1:210110974-210111310	HepG2	liver:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
20	CHD1	chr1:210110861-210112436	H1-hESC	embryonic stem cell:	n/a	chr1:210111320-210111330
21	REST	chr1:210110459-210111899	PFSK-1	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
22	REST	chr1:210110687-210111901	SK-N-SH	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
23	RCOR1	chr1:210110849-210111509	IMR90	lung:	n/a	n/a
24	REST	chr1:210110454-210112019	SK-N-SH	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111898-210111905 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
25	REST	chr1:210110783-210111431	MCF-7	breast:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
26	TEAD4	chr1:210110859-210111443	A549	lung:	n/a	n/a
27	REST	chr1:210110737-210111331	HepG2	liver:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
28	REST	chr1:210110656-210112046	U87	brain:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111898-210111905 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
29	REST	chr1:210110700-210111281	HCT-116	colon:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
30	REST	chr1:210110744-210111328	K562	blood:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
31	SIN3AK20	chr1:210111041-210111252	SK-N-SH	brain:	n/a	n/a
32	JUND	chr1:210110209-210112774	SK-N-SH	brain:	n/a	chr1:210111772-210111781
33	USF1	chr1:210111078-210111610	H1-hESC	embryonic stem cell:	n/a	chr1:210111382-210111391 chr1:210111381-210111390 chr1:210111383-210111392 chr1:210111382-210111391
34	REST	chr1:210110524-210111516	HL-60	blood:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
35	MXI1	chr1:210110276-210113314	SK-N-SH	brain:	n/a	n/a
36	REST	chr1:210110643-210111333	H1-hESC	embryonic stem cell:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
37	REST	chr1:210110651-210112405	H1-neurons	neurons:	n/a	chr1:210111591-210111604 chr1:210111694-210111707 chr1:210111126-210111144 chr1:210111586-210111599 chr1:210111898-210111905 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111676-210111689 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
38	HDAC2	chr1:210110920-210111324	H1-hESC	embryonic stem cell:	n/a	chr1:210111125-210111144
39	MAX	chr1:210110774-210111642	H1-hESC	embryonic stem cell:	n/a	chr1:210111382-210111391
40	E2F4	chr1:210110965-210111247	MCF10A-Er-Src	breast:	n/a	chr1:210111211-210111221
41	ELF1	chr1:210111102-210111329	GM12878	blood:	n/a	n/a
42	RAD21	chr1:210110953-210111299	IMR90	lung:	n/a	n/a
43	SIN3AK20	chr1:210110860-210111353	SK-N-SH	brain:	n/a	n/a
44	USF2	chr1:210111103-210111569	H1-hESC	embryonic stem cell:	n/a	chr1:210111382-210111391 chr1:210111381-210111390 chr1:210111383-210111392 chr1:210111382-210111391
45	BCLAF1	chr1:210111028-210111270	GM12878	blood:	n/a	chr1:210111130-210111139
46	REST	chr1:210110401-210111450	A549	lung:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139
47	POLR2A	chr1:210110712-210112001	H1-neurons	neurons:	n/a	n/a
48	RUNX3	chr1:210110914-210111292	GM12878	blood:	n/a	n/a
49	USF1	chr1:210111122-210111685	SK-N-SH_RA	brain:	n/a	chr1:210111382-210111391 chr1:210111381-210111390 chr1:210111383-210111392 chr1:210111382-210111391
50	REST	chr1:210110459-210111476	ECC-1	luminal epithelium:	n/a	chr1:210111126-210111144 chr1:210111125-210111145 chr1:210111128-210111141 chr1:210111125-210111145 chr1:210111131-210111145 chr1:210111130-210111139

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRF6-1	chr1:210107873-210111294	NONHSAT009248

Variant related genes	Relation type
SYT14	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10127635	1.00[EUR][1000 genomes]
rs1016480	1.00[EUR][1000 genomes]
rs1016481	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10863808	1.00[EUR][1000 genomes]
rs11119380	1.00[EUR][1000 genomes]
rs11119393	1.00[EUR][1000 genomes]
rs11119395	1.00[EUR][1000 genomes]
rs11119402	1.00[EUR][1000 genomes]
rs11119404	1.00[EUR][1000 genomes]
rs11119408	1.00[EUR][1000 genomes]
rs11119411	1.00[EUR][1000 genomes]
rs11801400	1.00[EUR][1000 genomes]
rs11810848	1.00[EUR][1000 genomes]
rs11811996	1.00[EUR][1000 genomes]
rs12059259	1.00[EUR][1000 genomes]
rs12073806	1.00[EUR][1000 genomes]
rs12078871	1.00[EUR][1000 genomes]
rs12079711	1.00[EUR][1000 genomes]
rs12080332	1.00[EUR][1000 genomes]
rs12082067	1.00[EUR][1000 genomes]
rs12085355	1.00[EUR][1000 genomes]
rs12086145	1.00[EUR][1000 genomes]
rs12089636	1.00[EUR][1000 genomes]
rs12090781	1.00[EUR][1000 genomes]
rs12092551	1.00[EUR][1000 genomes]
rs12093254	1.00[EUR][1000 genomes]
rs12239153	1.00[EUR][1000 genomes]
rs12239590	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239724	1.00[EUR][1000 genomes]
rs1334572	1.00[EUR][1000 genomes]
rs13376651	1.00[EUR][1000 genomes]
rs1413698	1.00[EUR][1000 genomes]
rs1591300	1.00[EUR][1000 genomes]
rs1602289	1.00[EUR][1000 genomes]
rs17015476	1.00[EUR][1000 genomes]
rs17015480	1.00[EUR][1000 genomes]
rs17015532	1.00[EUR][1000 genomes]
rs17015561	1.00[EUR][1000 genomes]
rs17015638	1.00[EUR][1000 genomes]
rs17015652	1.00[EUR][1000 genomes]
rs17041975	1.00[EUR][1000 genomes]
rs2018942	1.00[EUR][1000 genomes]
rs2130626	1.00[EUR][1000 genomes]
rs2130627	1.00[EUR][1000 genomes]
rs2130628	1.00[EUR][1000 genomes]
rs2171988	1.00[EUR][1000 genomes]
rs34400113	1.00[EUR][1000 genomes]
rs35046399	1.00[EUR][1000 genomes]
rs56075770	1.00[EUR][1000 genomes]
rs56105015	1.00[EUR][1000 genomes]
rs56271040	1.00[EUR][1000 genomes]
rs56733441	1.00[EUR][1000 genomes]
rs57082045	1.00[EUR][1000 genomes]
rs57790572	1.00[EUR][1000 genomes]
rs58701658	0.91[AMR][1000 genomes]
rs58775140	1.00[EUR][1000 genomes]
rs59230578	1.00[EUR][1000 genomes]
rs61049229	1.00[EUR][1000 genomes]
rs61644695	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6540577	1.00[EUR][1000 genomes]
rs6689269	1.00[EUR][1000 genomes]
rs6692822	1.00[EUR][1000 genomes]
rs73066422	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73066498	1.00[EUR][1000 genomes]
rs73068419	1.00[EUR][1000 genomes]
rs73072224	1.00[EUR][1000 genomes]
rs74156272	1.00[EUR][1000 genomes]
rs7512760	1.00[EUR][1000 genomes]
rs7515629	1.00[EUR][1000 genomes]
rs7523089	1.00[EUR][1000 genomes]
rs7530907	1.00[EUR][1000 genomes]
rs7536495	1.00[EUR][1000 genomes]
rs7556078	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs970788	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs978754	1.00[EUR][1000 genomes]
rs9803620	1.00[EUR][1000 genomes]
rs9970894	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1825811	chr1:210082206-210135806	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3438109	chr1:210110354-210112902	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210110200-210112400	Active TSS	Brain Anterior Caudate	brain
2	chr1:210110200-210112800	Active TSS	Brain Angular Gyrus	brain
3	chr1:210110400-210112400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:210110400-210112800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:210110400-210112800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:210110600-210111600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:210110600-210111600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:210110600-210112000	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr1:210110600-210112000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:210110600-210112000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:210110600-210112000	Active TSS	Brain Cingulate Gyrus	brain
12	chr1:210110600-210112200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:210110600-210112200	Bivalent/Poised TSS	Osteobl	bone
14	chr1:210110600-210112400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:210110600-210112600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:210110600-210112800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:210110600-210113000	Active TSS	Fetal Brain Female	brain
18	chr1:210110600-210113200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:210110800-210111400	Bivalent Enhancer	Esophagus	oesophagus
20	chr1:210110800-210111600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:210110800-210111600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:210110800-210111800	Bivalent Enhancer	Liver	Liver
23	chr1:210110800-210112000	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:210110800-210112000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:210110800-210112000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:210110800-210112000	Active TSS	Brain Germinal Matrix	brain
27	chr1:210110800-210112000	Bivalent Enhancer	Small Intestine	intestine
28	chr1:210110800-210112000	Bivalent/Poised TSS	HSMMtube	muscle
29	chr1:210110800-210112000	Active TSS	NHLF	lung
30	chr1:210110800-210112200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:210110800-210112200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:210110800-210112200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:210110800-210112200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:210110800-210112200	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:210110800-210112400	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:210110800-210112400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:210110800-210112400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:210111000-210111400	Active TSS	Primary hematopoietic stem cells	blood
39	chr1:210111000-210111400	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
40	chr1:210111000-210111400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:210111000-210111400	Active TSS	Pancreas	Pancrea
42	chr1:210111000-210111600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:210111000-210111600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr1:210111000-210111600	Active TSS	HSMM	muscle
45	chr1:210111000-210111800	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:210111000-210111800	Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr1:210111000-210112000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:210111000-210112000	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:210111000-210112000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
50	chr1:210111000-210112000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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