Variant report

Variant	rs2359322
Chromosome Location	chr1:212989107-212989108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212986600..212989235-chr1:213030292..213032089,2	K562	blood:
2	chr1:212987979..212990902-chr1:213030404..213032283,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10494955	0.90[ASN][1000 genomes]
rs1054733	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10863990	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863993	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863995	0.81[ASN][1000 genomes]
rs10863998	0.89[ASN][1000 genomes]
rs10863999	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864000	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864001	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120011	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120012	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120013	0.86[ASN][1000 genomes]
rs11120019	0.85[ASN][1000 genomes]
rs11120024	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120025	0.82[ASN][1000 genomes]
rs11120026	0.88[ASN][1000 genomes]
rs11120027	0.88[ASN][1000 genomes]
rs11120032	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120037	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11120039	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12064985	0.86[ASN][1000 genomes]
rs12088916	0.88[ASN][1000 genomes]
rs12095846	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12097897	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12125321	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12126017	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12132316	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12136046	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12136834	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565557	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12722742	0.88[ASN][1000 genomes]
rs12734406	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12734543	0.99[ASN][1000 genomes]
rs12737398	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12741704	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12743402	0.83[ASN][1000 genomes]
rs12744602	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12747251	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3820679	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3862953	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951463	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951638	0.86[ASN][1000 genomes]
rs6540761	0.84[EUR][1000 genomes]
rs6540763	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6661720	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669492	0.80[ASN][1000 genomes]
rs6679350	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679549	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6689604	0.94[ASN][1000 genomes]
rs6690689	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6693311	0.88[ASN][1000 genomes]
rs6694452	0.81[ASN][1000 genomes]
rs6697507	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700410	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6702025	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6702611	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7554105	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556272	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2359322	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs2359322	NSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
3	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
4	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
5	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
6	chr1:212967200-212989600	Weak transcription	NHLF	lung
7	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:212970600-212989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:212971000-212989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:212972600-212989800	Weak transcription	HSMMtube	muscle
13	chr1:212972600-212990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:212975600-212989600	Weak transcription	Brain Angular Gyrus	brain
15	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
16	chr1:212976000-212989600	Weak transcription	HSMM	muscle
17	chr1:212976000-212989600	Weak transcription	K562	blood
18	chr1:212976000-212990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:212976000-212990200	Weak transcription	Fetal Brain Female	brain
20	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:212978200-212989600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:212978200-212989800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:212978400-212989800	Weak transcription	Brain Germinal Matrix	brain
24	chr1:212979200-212994200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:212979600-212989800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:212979600-212992000	Weak transcription	Brain Anterior Caudate	brain
27	chr1:212979600-212993200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:212980000-212989600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:212981000-212990400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:212981600-212990400	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:212982400-212989600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:212982400-212990400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:212982600-212989600	Weak transcription	Fetal Lung	lung
36	chr1:212982600-212990000	Weak transcription	Hela-S3	cervix
37	chr1:212982600-212990400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:212982600-212992800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:212982800-212989800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:212982800-212989800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:212982800-212992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:212982800-212992600	Weak transcription	Placenta	Placenta
43	chr1:212984800-212989600	Weak transcription	Fetal Stomach	stomach
44	chr1:212985400-212989400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr1:212986800-212989800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:212987000-212992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:212987200-212993000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:212987400-212991200	Enhancers	Fetal Intestine Large	intestine
49	chr1:212987800-212989800	Enhancers	A549	lung
50	chr1:212988200-212990000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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