Variant report

Variant	rs12064985
Chromosome Location	chr1:212966176-212966177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:212964236-212966381	SK-N-SH	brain:	n/a	n/a
2	JUN	chr1:212965965-212967572	K562	blood:	n/a	n/a
3	POLR2A	chr1:212964707-212966225	HepG2	liver:	n/a	n/a
4	HEY1	chr1:212966132-212966504	HepG2	liver:	n/a	n/a
5	HEY1	chr1:212964642-212966436	K562	blood:	n/a	chr1:212965247-212965262 chr1:212965244-212965259
6	POLR2A	chr1:212964765-212966177	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212965461..212968054-chr1:213031452..213034127,2	MCF-7	breast:
2	chr1:212963280..212966676-chr1:213030010..213031803,4	K562	blood:
3	chr1:212965176..212966735-chr1:213030010..213031816,2	K562	blood:
4	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
5	chr1:212587143..212589756-chr1:212965630..212967810,2	K562	blood:
6	chr1:212965435..212968040-chr1:213139784..213142502,2	K562	blood:
7	chr1:212964912..212966461-chr1:212995791..212998620,2	K562	blood:
8	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:
9	chr1:212525375..212527593-chr1:212964320..212966298,2	MCF-7	breast:
10	chr1:212586665..212588349-chr1:212964322..212966191,2	MCF-7	breast:
11	chr1:212779632..212786722-chr1:212965265..212968763,9	K562	blood:

No data

Variant related genes	Relation type
NSL1	TF binding region
TATDN3	TF binding region
ENSG00000203705	Chromatin interaction
ENSG00000201544	Chromatin interaction
ENSG00000143494	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000236905	Chromatin interaction
ENSG00000065600	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10494955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1054733	0.87[ASN][1000 genomes]
rs10863990	0.87[ASN][1000 genomes]
rs10863993	0.92[ASN][1000 genomes]
rs10863995	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10863998	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863999	0.95[ASN][1000 genomes]
rs10864000	0.86[ASN][1000 genomes]
rs10864001	0.86[ASN][1000 genomes]
rs11120011	0.89[ASN][1000 genomes]
rs11120012	0.90[ASN][1000 genomes]
rs11120013	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120019	0.88[ASN][1000 genomes]
rs11120024	0.93[ASN][1000 genomes]
rs11120025	0.91[ASN][1000 genomes]
rs11120026	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120027	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120032	0.83[ASN][1000 genomes]
rs11120037	0.84[ASN][1000 genomes]
rs11120039	0.83[ASN][1000 genomes]
rs1133462	0.86[ASN][1000 genomes]
rs12088916	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12095846	0.84[ASN][1000 genomes]
rs12097897	0.95[ASN][1000 genomes]
rs12125321	0.85[ASN][1000 genomes]
rs12126017	0.95[ASN][1000 genomes]
rs12130945	0.86[ASN][1000 genomes]
rs12132316	0.90[ASN][1000 genomes]
rs12136046	0.92[ASN][1000 genomes]
rs12136834	0.92[ASN][1000 genomes]
rs12722742	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12734543	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12737398	0.86[ASN][1000 genomes]
rs12741704	0.98[ASN][1000 genomes]
rs12743402	0.88[ASN][1000 genomes]
rs12744602	0.85[ASN][1000 genomes]
rs12747251	0.83[ASN][1000 genomes]
rs2359322	0.86[ASN][1000 genomes]
rs3820679	0.98[ASN][1000 genomes]
rs3862953	0.86[ASN][1000 genomes]
rs4951460	0.81[EUR][1000 genomes]
rs4951463	0.98[ASN][1000 genomes]
rs4951638	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61829243	0.87[ASN][1000 genomes]
rs6540761	0.85[ASN][1000 genomes]
rs6540763	0.90[ASN][1000 genomes]
rs6661720	0.92[ASN][1000 genomes]
rs6669492	0.83[ASN][1000 genomes]
rs6679350	0.98[ASN][1000 genomes]
rs6679549	0.98[ASN][1000 genomes]
rs6689604	0.84[ASN][1000 genomes]
rs6690689	0.92[ASN][1000 genomes]
rs6693311	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6694452	0.85[ASN][1000 genomes]
rs6697507	0.84[ASN][1000 genomes]
rs6700410	0.84[ASN][1000 genomes]
rs6702025	0.85[ASN][1000 genomes]
rs6702611	0.95[ASN][1000 genomes]
rs7554105	0.86[ASN][1000 genomes]
rs7556272	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1010003	chr1:212944240-212986996	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12064985	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12064985	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs12064985	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs12064985	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs12064985	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs12064985	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212963200-212966200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:212963200-212966600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:212963400-212966400	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:212963600-212966400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:212963800-212966200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:212963800-212966200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:212963800-212966200	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:212963800-212966400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:212963800-212966400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:212963800-212966600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:212964000-212966200	Active TSS	Colon Smooth Muscle	Colon
12	chr1:212964000-212966200	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr1:212964200-212966200	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:212964200-212966200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:212964200-212966200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:212964200-212966200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:212964200-212966200	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:212964200-212966200	Active TSS	Fetal Kidney	kidney
19	chr1:212964200-212966200	Active TSS	Ovary	ovary
20	chr1:212964200-212966200	Active TSS	Psoas Muscle	Psoas
21	chr1:212964200-212966200	Active TSS	GM12878-XiMat	blood
22	chr1:212964200-212966400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:212964200-212966400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:212964200-212966400	Active TSS	Fetal Brain Female	brain
25	chr1:212964200-212966400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:212964200-212966400	Active TSS	NH-A	brain
27	chr1:212964400-212966200	Active TSS	Colonic Mucosa	Colon
28	chr1:212964400-212966200	Active TSS	Right Ventricle	heart
29	chr1:212964600-212966200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:212964600-212966200	Active TSS	Brain Cingulate Gyrus	brain
31	chr1:212964600-212966200	Active TSS	Brain Substantia Nigra	brain
32	chr1:212964600-212966200	Active TSS	HSMM	muscle
33	chr1:212964600-212966200	Active TSS	NHEK	skin
34	chr1:212965200-212966200	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr1:212965400-212966200	Active TSS	Right Atrium	heart
36	chr1:212965400-212966200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr1:212965400-212966400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr1:212965400-212966400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr1:212965400-212966400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:212965400-212966600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:212965600-212966400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:212965600-212966400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr1:212965800-212966200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr1:212965800-212966200	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:212965800-212966200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr1:212965800-212966200	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr1:212965800-212966200	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr1:212965800-212966200	Flanking Active TSS	Fetal Thymus	thymus
49	chr1:212965800-212966200	Enhancers	Stomach Mucosa	stomach
50	chr1:212965800-212966200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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