Variant report

Variant	rs6540768
Chromosome Location	chr1:213032907-213032908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:213032764-213032941	HepG2	liver:	n/a	n/a
2	GATA1	chr1:213032868-213034975	K562	blood:	n/a	chr1:213033557-213033570 chr1:213033559-213033566
3	POLR2A	chr1:213030204-213032910	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:213032255..213037228-chr1:213037322..213040248,4	K562	blood:
2	chr1:213027721..213030641-chr1:213032667..213035705,3	K562	blood:
3	chr1:213029061..213031968-chr1:213032486..213034078,2	K562	blood:
4	chr1:213025871..213028763-chr1:213030169..213033277,3	MCF-7	breast:
5	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:
6	chr1:212965461..212968054-chr1:213031452..213034127,2	MCF-7	breast:
7	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
8	chr1:212977806..212980707-chr1:213030715..213033244,2	K562	blood:
9	chr1:213030101..213032938-chr1:213186047..213190102,3	K562	blood:
10	chr1:213031674..213033675-chr1:213035938..213038632,2	MCF-7	breast:

No data

Variant related genes	Relation type
FLVCR1-AS1	TF binding region
FLVCR1	TF binding region
ENSG00000236317	TF binding region
ENSG00000236317	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000174606	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000235182	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10127459	1.00[ASN][1000 genomes]
rs10746436	1.00[ASN][1000 genomes]
rs10779594	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864003	1.00[ASN][1000 genomes]
rs10864013	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864017	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10864019	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120033	1.00[ASN][1000 genomes]
rs12036735	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1284800	1.00[ASN][1000 genomes]
rs1284864	1.00[ASN][1000 genomes]
rs1615680	1.00[ASN][1000 genomes]
rs1692178	1.00[ASN][1000 genomes]
rs1692179	1.00[ASN][1000 genomes]
rs1692180	1.00[ASN][1000 genomes]
rs17020044	1.00[ASN][1000 genomes]
rs17020046	1.00[ASN][1000 genomes]
rs1770777	1.00[ASN][1000 genomes]
rs1770778	1.00[ASN][1000 genomes]
rs1874419	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047289	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047292	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2047293	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359324	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2456815	1.00[ASN][1000 genomes]
rs2644545	1.00[ASN][1000 genomes]
rs2792558	1.00[ASN][1000 genomes]
rs2792560	1.00[ASN][1000 genomes]
rs2792561	1.00[ASN][1000 genomes]
rs35976699	1.00[ASN][1000 genomes]
rs41315581	1.00[ASN][1000 genomes]
rs4418676	0.95[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4951468	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4951649	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59252582	1.00[ASN][1000 genomes]
rs6666362	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667161	1.00[ASN][1000 genomes]
rs6674933	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688865	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6689134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703612	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528119	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533932	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7542906	1.00[ASN][1000 genomes]
rs963327	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6540768	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs6540768	FLVCR1-AS1	cis	Whole Blood	GTEx
rs6540768	FLVCR1-AS1	cis	Heart Left Ventricle	GTEx
rs6540768	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs6540768	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs6540768	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs6540768	FLVCR1-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 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	chr1:213030400-213033400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:213030400-213034000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:213030400-213034000	Active TSS	HSMM	muscle
6	chr1:213030400-213034600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:213030400-213035600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:213030600-213033000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:213030600-213033200	Active TSS	A549	lung
10	chr1:213030600-213033800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:213030600-213034000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:213030600-213034000	Active TSS	GM12878-XiMat	blood
13	chr1:213030600-213034400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:213030600-213035000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:213030800-213033400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:213030800-213033400	Active TSS	HSMMtube	muscle
17	chr1:213030800-213033800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr1:213030800-213033800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:213030800-213034200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:213030800-213035200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:213031000-213033400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:213031200-213033200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:213031200-213033400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:213031800-213033600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:213032000-213033200	Active TSS	Brain Germinal Matrix	brain
26	chr1:213032000-213033400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr1:213032000-213033600	Flanking Active TSS	HMEC	breast
28	chr1:213032000-213034000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:213032000-213034000	Flanking Active TSS	Dnd41	blood
30	chr1:213032200-213033000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:213032200-213033000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:213032200-213033000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr1:213032200-213033000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr1:213032200-213033000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:213032200-213033000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:213032200-213033000	Flanking Active TSS	Fetal Stomach	stomach
37	chr1:213032200-213033200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr1:213032200-213033400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:213032200-213033400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:213032200-213033600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:213032200-213033600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:213032200-213033600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:213032200-213033600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:213032200-213033600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr1:213032200-213034000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:213032200-213034200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr1:213032400-213033000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:213032400-213033000	Enhancers	Aorta	Aorta
49	chr1:213032400-213034600	Enhancers	Spleen	Spleen
50	chr1:213032600-213033000	Enhancers	Thymus	Thymus

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