Variant report

Variant	rs2201601
Chromosome Location	chr1:213031448-213031449
allele	C/G
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	CREB1	chr1:213030786-213032031	GM12878	blood:	n/a	n/a
2	BCLAF1	chr1:213031065-213031792	GM12878	blood:	n/a	chr1:213031757-213031766 chr1:213031597-213031610
3	ZBTB7A	chr1:213030931-213032339	K562	blood:	n/a	n/a
4	JUND	chr1:213031147-213031805	A549	lung:	n/a	chr1:213031526-213031535 chr1:213031462-213031471
5	MAX	chr1:213031038-213031603	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:213031024-213031871	HUVEC	blood vessel:	n/a	n/a
7	TBL1XR1	chr1:213031030-213031772	K562	blood:	n/a	n/a
8	SIN3AK20	chr1:213030942-213032476	PANC-1	pancreas:	n/a	n/a
9	FOXP2	chr1:213031323-213031860	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr1:213031027-213032759	MCF10A-Er-Src	breast:	n/a	n/a
11	HA-E2F1	chr1:213031256-213032467	Hela-S3	cervix:	n/a	chr1:213031461-213031470 chr1:213031528-213031537 chr1:213031516-213031523
12	TAF1	chr1:213030944-213031874	H1-hESC	embryonic stem cell:	n/a	n/a
13	HDAC2	chr1:213030916-213031817	HepG2	liver:	n/a	n/a
14	E2F1	chr1:213031245-213032415	Hela-S3	cervix:	n/a	chr1:213031461-213031470 chr1:213031528-213031537 chr1:213031516-213031523
15	ZNF384	chr1:213030549-213031823	K562	blood:	n/a	n/a
16	USF1	chr1:213031412-213031696	SK-N-SH_RA	brain:	n/a	n/a
17	SIN3AK20	chr1:213031017-213031540	PANC-1	pancreas:	n/a	n/a
18	TAF1	chr1:213030865-213031797	K562	blood:	n/a	n/a
19	SP1	chr1:213031233-213031736	H1-hESC	embryonic stem cell:	n/a	chr1:213031571-213031580 chr1:213031460-213031474 chr1:213031517-213031538 chr1:213031569-213031581 chr1:213031569-213031581 chr1:213031565-213031578 chr1:213031695-213031709 chr1:213031461-213031470 chr1:213031459-213031470
20	BACH1	chr1:213031013-213032131	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr1:213030857-213032406	GM18505	blood:	n/a	n/a
22	E2F4	chr1:213031044-213031784	MCF10A-Er-Src	breast:	n/a	chr1:213031461-213031470 chr1:213031528-213031537 chr1:213031516-213031523
23	UBTF	chr1:213030900-213032562	K562	blood:	n/a	n/a
24	RAD21	chr1:213031037-213031736	HepG2	liver:	n/a	n/a
25	FOXP2	chr1:213031433-213031697	SK-N-MC	brain:	n/a	n/a
26	MAX	chr1:213030940-213032497	SK-N-SH	brain:	n/a	chr1:213031632-213031639
27	FOXM1	chr1:213031198-213031694	GM12878	blood:	n/a	n/a
28	EGR1	chr1:213031297-213031764	GM12878	blood:	n/a	chr1:213031604-213031617 chr1:213031460-213031470 chr1:213031456-213031469
29	POLR2A	chr1:213031284-213031853	A549	lung:	n/a	n/a
30	MXI1	chr1:213031161-213032353	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:213031007-213031769	HCT-116	colon:	n/a	n/a
32	ZNF143	chr1:213031203-213032526	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:213031139-213032523	MCF-7	breast:	n/a	n/a
34	HCFC1	chr1:213030774-213032525	Hela-S3	cervix:	n/a	n/a
35	MXI1	chr1:213030966-213032442	HepG2	liver:	n/a	n/a
36	ZNF263	chr1:213030951-213032903	HEK293-T-REx	kidney:	n/a	chr1:213031610-213031619
37	POLR2A	chr1:213029909-213032745	GM12891	blood:	n/a	n/a
38	REST	chr1:213031423-213031761	SK-N-SH	brain:	n/a	n/a
39	CREB1	chr1:213030803-213031879	A549	lung:	n/a	n/a
40	CCNT2	chr1:213031017-213032445	K562	blood:	n/a	n/a
41	SP2	chr1:213031374-213031698	K562	blood:	n/a	chr1:213031565-213031580
42	POLR2A	chr1:213030952-213032496	GM12878	blood:	n/a	n/a
43	CHD2	chr1:213031004-213031839	HepG2	liver:	n/a	chr1:213031608-213031618 chr1:213031516-213031523
44	E2F6	chr1:213030992-213032473	A549	lung:	n/a	chr1:213031461-213031470 chr1:213031528-213031537 chr1:213031516-213031523
45	POLR2A	chr1:213030920-213031918	GM12892	blood:	n/a	n/a
46	ELF1	chr1:213031280-213031797	K562	blood:	n/a	n/a
47	ZBTB33	chr1:213031251-213031795	K562	blood:	n/a	chr1:213031501-213031511
48	POLR2A	chr1:213031123-213031854	PANC-1	pancreas:	n/a	n/a
49	TEAD4	chr1:213030852-213031670	HepG2	liver:	n/a	n/a
50	GATA3	chr1:213030830-213032386	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:213026064..213028809-chr1:213029690..213032627,2	K562	blood:
2	chr1:213025871..213028763-chr1:213030169..213033277,3	MCF-7	breast:
3	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:
4	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
5	chr1:212977806..212980707-chr1:213030715..213033244,2	K562	blood:
6	chr1:213031210..213032182-chr8:145641945..145642591,2	HCT-116	colon:
7	chr1:213030101..213032938-chr1:213186047..213190102,3	K562	blood:
8	chr1:213019184..213021421-chr1:213029036..213031526,2	K562	blood:
9	chr1:212965176..212966735-chr1:213030010..213031816,2	K562	blood:
10	chr1:212963280..212966676-chr1:213030010..213031803,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf227-1	chr1:213031108-213031452	XLOC_001197
2	lnc-C1orf227-1	chr1:213031108-213031480	XLOC_001197
3	lnc-C1orf227-1	chr1:213031108-213031480	NONHSAT009410
4	lnc-C1orf227-1	chr1:213031108-213031480	NONHSAT009411

Variant related genes	Relation type
ENSG00000236317	TF binding region
FLVCR1	TF binding region
FLVCR1-AS1	TF binding region
ENSG00000185523	Chromatin interaction
ENSG00000147804	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000174606	Chromatin interaction
ENSG00000235182	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000236317	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10779588	0.81[AMR][1000 genomes]
rs10864010	0.81[AMR][1000 genomes]
rs10864023	0.80[EUR][1000 genomes]
rs10864028	0.91[EUR][1000 genomes]
rs10864029	0.90[EUR][1000 genomes]
rs11120042	0.80[AMR][1000 genomes]
rs11120044	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120049	0.81[AMR][1000 genomes]
rs11120062	0.80[EUR][1000 genomes]
rs11582817	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11586464	0.89[EUR][1000 genomes]
rs12023052	0.81[AMR][1000 genomes]
rs12140831	0.81[AMR][1000 genomes]
rs12404754	0.80[EUR][1000 genomes]
rs12405293	0.80[EUR][1000 genomes]
rs12567976	0.80[EUR][1000 genomes]
rs12754609	0.80[EUR][1000 genomes]
rs12755947	0.80[EUR][1000 genomes]
rs1587175	0.80[EUR][1000 genomes]
rs2279692	0.82[AMR][1000 genomes]
rs2359325	0.80[EUR][1000 genomes]
rs3207090	0.80[EUR][1000 genomes]
rs4951474	0.80[EUR][1000 genomes]
rs6670064	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs963328	0.81[AMR][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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs2201601	FLVCR1-AS1	cis	Esophagus Mucosa	GTEx
rs2201601	FLVCR1-AS1	cis	Thyroid	GTEx
rs2201601	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs2201601	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs2201601	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs2201601	FLVCR1-AS1	cis	Stomach	GTEx
rs2201601	FLVCR1	cis	multi-tissue	Pritchard
rs2201601	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs2201601	FLVCR1-AS1	cis	Artery Tibial	GTEx
rs2201601	FLVCR1-AS1	cis	Whole Blood	GTEx
rs2201601	FLVCR1-AS1	cis	Muscle Skeletal	GTEx
rs2201601	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs2201601	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs2201601	VASH2	Cis_1M	lymphoblastoid	RTeQTL
rs2201601	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs2201601	FLVCR1-AS1	cis	lung	GTEx
rs2201601	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs2201601	NSL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213029600-213033200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:213029600-213033400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:213029800-213032000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:213030000-213032800	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:213030400-213031800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:213030400-213032200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:213030400-213032200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:213030400-213033400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:213030400-213034000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:213030400-213034000	Active TSS	HSMM	muscle
11	chr1:213030400-213034600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:213030400-213035600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr1:213030600-213032000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:213030600-213032000	Active TSS	HMEC	breast
15	chr1:213030600-213032200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:213030600-213032200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:213030600-213032200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:213030600-213032200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:213030600-213032200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr1:213030600-213032200	Active TSS	Right Ventricle	heart
21	chr1:213030600-213033000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:213030600-213033200	Active TSS	A549	lung
23	chr1:213030600-213033800	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:213030600-213034000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr1:213030600-213034000	Active TSS	GM12878-XiMat	blood
26	chr1:213030600-213034400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:213030600-213035000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:213030800-213031600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:213030800-213032200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:213030800-213032200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:213030800-213032200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:213030800-213032200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:213030800-213032200	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:213030800-213032200	Active TSS	Brain Angular Gyrus	brain
35	chr1:213030800-213032200	Active TSS	Brain Anterior Caudate	brain
36	chr1:213030800-213032200	Active TSS	Brain Hippocampus Middle	brain
37	chr1:213030800-213032200	Active TSS	Brain Substantia Nigra	brain
38	chr1:213030800-213032200	Active TSS	Fetal Brain Female	brain
39	chr1:213030800-213032200	Active TSS	Fetal Stomach	stomach
40	chr1:213030800-213032200	Active TSS	Left Ventricle	heart
41	chr1:213030800-213032200	Active TSS	Ovary	ovary
42	chr1:213030800-213032200	Active TSS	Pancreas	Pancrea
43	chr1:213030800-213032200	Active TSS	Thymus	Thymus
44	chr1:213030800-213032200	Active TSS	Hela-S3	cervix
45	chr1:213030800-213032200	Active TSS	NHEK	skin
46	chr1:213030800-213032400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:213030800-213032400	Active TSS	Brain Cingulate Gyrus	brain
48	chr1:213030800-213032400	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr1:213030800-213032400	Active TSS	Fetal Heart	heart
50	chr1:213030800-213032400	Active TSS	NHDF-Ad	bronchial

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