Variant report

Variant	rs11120025
Chromosome Location	chr1:212955231-212955232
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212781936..212785514-chr1:212953111..212956420,3	K562	blood:
2	chr1:212880638..212882671-chr1:212954143..212956179,2	K562	blood:
3	chr1:212953290..212958548-chr1:212960806..212967767,9	K562	blood:
4	chr1:212782588..212784090-chr1:212954271..212956784,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10494955	0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs1054733	0.80[ASN][1000 genomes]
rs10863990	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863993	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863995	0.81[ASN][1000 genomes]
rs10863998	0.89[ASN][1000 genomes]
rs10863999	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864000	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10864001	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs11120002	0.87[AFR][1000 genomes]
rs11120011	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120012	0.94[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120013	0.86[ASN][1000 genomes]
rs11120019	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11120024	0.91[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11120026	0.93[ASN][1000 genomes]
rs11120027	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.93[ASN][1000 genomes]
rs11120037	0.87[ASN][1000 genomes]
rs11120039	0.86[ASN][1000 genomes]
rs1133462	0.82[ASN][1000 genomes]
rs12064985	0.91[ASN][1000 genomes]
rs12088916	0.87[ASN][1000 genomes]
rs12095846	0.87[ASN][1000 genomes]
rs12097897	0.81[CHB][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12125321	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12126017	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12130945	0.82[ASN][1000 genomes]
rs12132316	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12136046	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12136834	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12722742	0.87[ASN][1000 genomes]
rs12727790	0.86[AFR][1000 genomes]
rs12734543	0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12737398	0.82[ASN][1000 genomes]
rs12741704	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12743402	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12747251	0.91[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12758602	0.81[AFR][1000 genomes]
rs12759287	0.84[AFR][1000 genomes]
rs2359322	0.82[ASN][1000 genomes]
rs34274815	0.87[AFR][1000 genomes]
rs3820679	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3862953	0.82[ASN][1000 genomes]
rs4951457	0.86[YRI][hapmap]
rs4951463	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951636	0.84[AFR][1000 genomes]
rs4951637	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4951638	0.86[ASN][1000 genomes]
rs61829243	0.82[ASN][1000 genomes]
rs6540761	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6540763	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6661720	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669492	0.87[AFR][1000 genomes]
rs6679350	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679549	0.87[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689604	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6690689	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6693311	0.87[ASN][1000 genomes]
rs6694452	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6697507	0.86[ASN][1000 genomes]
rs6700410	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs6702025	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6702611	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7554105	0.82[ASN][1000 genomes]
rs7556272	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[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	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
6	nsv947467	chr1:212954839-212957948	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11120025	LQK1	cis	parietal	SCAN
rs11120025	VASH2	cis	parietal	SCAN
rs11120025	LQK1	cis	cerebellum	SCAN
rs11120025	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs11120025	NSL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 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	chr1:212923600-212956200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:212923800-212964200	Weak transcription	HMEC	breast
8	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
10	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:212928400-212956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:212936600-212956000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:212936600-212956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:212936600-212956200	Weak transcription	Thymus	Thymus
15	chr1:212936600-212959800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:212936600-212960200	Weak transcription	Lung	lung
17	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
18	chr1:212939400-212956200	Weak transcription	Fetal Stomach	stomach
19	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
20	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
21	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:212942800-212956400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:212943200-212956200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:212943200-212956200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:212943600-212957800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:212943800-212955400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:212944000-212956800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:212944000-212958000	Weak transcription	Brain Substantia Nigra	brain
31	chr1:212944200-212956000	Weak transcription	Primary T cells from cord blood	blood
32	chr1:212944200-212956200	Weak transcription	Psoas Muscle	Psoas
33	chr1:212944200-212956800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
35	chr1:212944400-212956200	Weak transcription	Fetal Muscle Leg	muscle
36	chr1:212945600-212956000	Weak transcription	NHLF	lung
37	chr1:212945800-212955800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:212945800-212959800	Weak transcription	Ovary	ovary
39	chr1:212947800-212956000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:212948200-212956000	Weak transcription	NHDF-Ad	bronchial
41	chr1:212948400-212956000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:212948400-212960000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:212949000-212955600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:212950800-212959800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:212951600-212956200	Weak transcription	HepG2	liver
47	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:212952400-212963000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:212952600-212963600	Weak transcription	Colonic Mucosa	Colon
50	chr1:212953000-212959800	Weak transcription	NHEK	skin

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