Variant report

Variant	rs10863990
Chromosome Location	chr1:212925601-212925602
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212903656..212906475-chr1:212923448..212926257,3	K562	blood:
2	chr1:212867492..212870204-chr1:212923902..212926371,2	K562	blood:
3	chr1:212924762..212928442-chr1:212932501..212935953,4	K562	blood:
4	chr1:212922257..212926037-chr1:212961956..212967117,4	K562	blood:

Variant related genes	Relation type
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494955	0.91[ASN][1000 genomes]
rs10863993	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863995	0.90[ASN][1000 genomes]
rs10863998	0.93[ASN][1000 genomes]
rs10863999	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864000	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10864001	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11120002	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11120011	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11120012	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120013	0.96[ASN][1000 genomes]
rs11120019	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120024	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120025	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11120026	0.88[ASN][1000 genomes]
rs11120027	0.88[ASN][1000 genomes]
rs11120032	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1133462	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12064985	0.87[ASN][1000 genomes]
rs12088916	0.94[ASN][1000 genomes]
rs12095846	0.80[EUR][1000 genomes]
rs12097897	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125321	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12126017	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130945	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12132316	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12136046	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136834	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12722742	0.94[ASN][1000 genomes]
rs12725274	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12727790	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12734543	0.83[ASN][1000 genomes]
rs12737398	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12741704	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12743402	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12747251	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12758602	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12759287	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2359322	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34274815	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3820679	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3862953	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4951463	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951636	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4951637	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4951638	0.96[ASN][1000 genomes]
rs61829227	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6540761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6540763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6661720	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669492	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6679350	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6679549	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690689	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6693311	0.94[ASN][1000 genomes]
rs6694452	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6702611	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7554105	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7556272	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	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
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10863990	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
2	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
3	chr1:212895600-212964600	Weak transcription	Gastric	stomach
4	chr1:212895800-212926200	Weak transcription	Hela-S3	cervix
5	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:212899800-212926400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:212900400-212927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:212900400-212932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:212900400-212936200	Weak transcription	Aorta	Aorta
10	chr1:212901400-212954000	Weak transcription	NH-A	brain
11	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney
12	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:212903600-212926400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:212904800-212926200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:212908000-212933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:212912000-212935800	Weak transcription	K562	blood
17	chr1:212912200-212925800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:212915000-212925800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:212915400-212932600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:212915400-212933400	Weak transcription	Ovary	ovary
21	chr1:212915400-212934400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:212915400-212936000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:212915400-212942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:212917400-212926400	Weak transcription	Thymus	Thymus
25	chr1:212917600-212931200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:212917800-212926000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:212918400-212929400	Weak transcription	Fetal Stomach	stomach
28	chr1:212918800-212930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:212919200-212925800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:212919600-212926400	Weak transcription	Right Atrium	heart
31	chr1:212920000-212929200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:212920600-212929400	Weak transcription	Fetal Intestine Small	intestine
33	chr1:212921000-212929400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:212922200-212939600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:212923000-212926200	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:212923400-212928600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr1:212923600-212925800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:212923600-212925800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:212923600-212926200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr1:212923600-212926200	Weak transcription	Brain Anterior Caudate	brain
41	chr1:212923600-212926200	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:212923600-212927600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:212923600-212927800	Weak transcription	Left Ventricle	heart
44	chr1:212923600-212932800	Weak transcription	Fetal Intestine Large	intestine
45	chr1:212923600-212935400	Weak transcription	Lung	lung
46	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
48	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:212923800-212925800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:212923800-212925800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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