Variant report

Variant	rs12743402
Chromosome Location	chr1:212949284-212949285
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212873155..212876101-chr1:212948012..212949658,2	K562	blood:
2	chr1:212946670..212949968-chr1:212963213..212965983,4	K562	blood:
3	chr1:212948302..212950579-chr1:212963223..212964976,2	K562	blood:
4	chr1:212947843..212950048-chr1:212956600..212958809,2	K562	blood:

Variant related genes	Relation type
ENSG00000117697	Chromatin interaction
ENSG00000123685	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10494955	0.91[ASN][1000 genomes]
rs1054733	0.81[ASN][1000 genomes]
rs10863990	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863993	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863995	0.95[ASN][1000 genomes]
rs10863998	0.93[ASN][1000 genomes]
rs10863999	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864000	0.83[ASN][1000 genomes]
rs10864001	0.83[ASN][1000 genomes]
rs11120002	0.82[EUR][1000 genomes]
rs11120011	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11120012	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120013	0.90[ASN][1000 genomes]
rs11120019	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120024	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120025	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11120026	0.88[ASN][1000 genomes]
rs11120027	0.88[ASN][1000 genomes]
rs11120032	0.85[ASN][1000 genomes]
rs1133462	0.83[ASN][1000 genomes]
rs12064985	0.88[ASN][1000 genomes]
rs12088916	0.91[ASN][1000 genomes]
rs12097897	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125321	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12126017	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12130945	0.83[ASN][1000 genomes]
rs12132316	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12136046	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12136834	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12722742	0.91[ASN][1000 genomes]
rs12725274	0.80[EUR][1000 genomes]
rs12727790	0.82[EUR][1000 genomes]
rs12734543	0.83[ASN][1000 genomes]
rs12737398	0.83[ASN][1000 genomes]
rs12741704	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12744602	0.82[ASN][1000 genomes]
rs12747251	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12759287	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2359322	0.83[ASN][1000 genomes]
rs3820679	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3862953	0.83[ASN][1000 genomes]
rs4951463	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951636	0.82[EUR][1000 genomes]
rs4951638	0.90[ASN][1000 genomes]
rs6540761	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6540763	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6661720	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6669492	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6679350	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6679549	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6690689	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693311	0.91[ASN][1000 genomes]
rs6694452	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702025	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6702611	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7554105	0.83[ASN][1000 genomes]
rs7556272	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12743402	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs12743402	NSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212901400-212954000	Weak transcription	NH-A	brain
4	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:212923800-212964200	Weak transcription	HMEC	breast
9	chr1:212924000-212954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:212926600-212954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:212926800-212954200	Weak transcription	Hela-S3	cervix
13	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
14	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:212928400-212954000	Weak transcription	Fetal Brain Male	brain
16	chr1:212928400-212956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:212928600-212954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:212934200-212952400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:212936600-212950600	Weak transcription	Placenta	Placenta
20	chr1:212936600-212954800	Weak transcription	Left Ventricle	heart
21	chr1:212936600-212956000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:212936600-212956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:212936600-212956200	Weak transcription	Thymus	Thymus
24	chr1:212936600-212959800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:212936600-212960200	Weak transcription	Lung	lung
26	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
27	chr1:212939400-212956200	Weak transcription	Fetal Stomach	stomach
28	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
29	chr1:212942400-212950400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
31	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:212942800-212956400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:212943000-212954200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:212943200-212953800	Weak transcription	HSMM	muscle
36	chr1:212943200-212954200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:212943200-212954200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:212943200-212956200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:212943200-212956200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:212943600-212954000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:212943600-212957800	Weak transcription	Brain Anterior Caudate	brain
43	chr1:212943800-212953800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:212943800-212954800	Weak transcription	Colon Smooth Muscle	Colon
45	chr1:212943800-212955400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:212944000-212954200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:212944000-212954600	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:212944000-212956800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:212944000-212958000	Weak transcription	Brain Substantia Nigra	brain
50	chr1:212944200-212949400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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