Variant report

Variant	rs11120027
Chromosome Location	chr1:212962207-212962208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212960294..212962883-chr1:213188555..213191323,2	K562	blood:
2	chr1:212793655..212795376-chr1:212961794..212963726,2	K562	blood:
3	chr1:212960922..212962804-chr1:212968235..212970840,2	K562	blood:
4	chr1:212949377..212951315-chr1:212960542..212962942,2	K562	blood:

Variant related genes	Relation type
ENSG00000174606	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10494955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1054733	0.85[ASN][1000 genomes]
rs10863990	0.88[ASN][1000 genomes]
rs10863993	0.93[ASN][1000 genomes]
rs10863995	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10863998	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863999	0.96[ASN][1000 genomes]
rs10864000	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10864001	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11120011	0.90[ASN][1000 genomes]
rs11120012	0.91[ASN][1000 genomes]
rs11120013	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11120019	0.90[ASN][1000 genomes]
rs11120024	0.80[ASW][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[ASN][1000 genomes]
rs11120025	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.93[ASN][1000 genomes]
rs11120026	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120032	0.85[ASN][1000 genomes]
rs11120037	0.86[ASN][1000 genomes]
rs11120039	0.84[ASN][1000 genomes]
rs1133462	0.88[ASN][1000 genomes]
rs12064985	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12088916	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12095846	0.86[ASN][1000 genomes]
rs12097897	0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12125321	0.86[ASN][1000 genomes]
rs12126017	0.96[ASN][1000 genomes]
rs12130945	0.88[ASN][1000 genomes]
rs12132316	0.92[ASN][1000 genomes]
rs12136046	0.93[ASN][1000 genomes]
rs12136834	0.93[ASN][1000 genomes]
rs12722742	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12734406	0.81[ASN][1000 genomes]
rs12734543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12737398	0.88[ASN][1000 genomes]
rs12741704	0.99[ASN][1000 genomes]
rs12743402	0.88[ASN][1000 genomes]
rs12744602	0.83[ASN][1000 genomes]
rs12747251	0.80[ASW][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs2359322	0.88[ASN][1000 genomes]
rs3820679	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs3862953	0.88[ASN][1000 genomes]
rs4951457	0.85[CEU][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap]
rs4951460	0.82[EUR][1000 genomes]
rs4951463	0.99[ASN][1000 genomes]
rs4951638	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61829243	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6540761	0.87[ASN][1000 genomes]
rs6540763	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs6661720	0.93[ASN][1000 genomes]
rs6669492	0.85[ASN][1000 genomes]
rs6679350	0.99[ASN][1000 genomes]
rs6679549	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs6689604	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs6690689	0.93[ASN][1000 genomes]
rs6693311	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6694452	0.86[ASN][1000 genomes]
rs6697507	0.85[ASN][1000 genomes]
rs6700410	0.94[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6702025	0.86[ASN][1000 genomes]
rs6702611	0.96[ASN][1000 genomes]
rs7554105	0.88[ASN][1000 genomes]
rs7556272	0.93[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11120027	LQK1	cis	parietal	SCAN
rs11120027	FLVCR1-AS1	cis	Artery Aorta	GTEx
rs11120027	LQK1	cis	lesional skin	skin_eQTL
rs11120027	LQK1	cis	cerebellum	SCAN
rs11120027	C1orf227	cis	parietal	SCAN
rs11120027	C1orf227	cis	cerebellum	SCAN
rs11120027	FLVCR1-AS1	cis	Nerve Tibial	GTEx
rs11120027	FLVCR1-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs11120027	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs11120027	BPIL3	trans	cerebellum	SCAN
rs11120027	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs11120027	VASH2	cis	parietal	SCAN
rs11120027	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs11120027	NSL1	cis	lymphoblastoid	seeQTL
rs11120027	LQK1	cis	uninvolved skin	skin_eQTL
rs11120027	C4BPA	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:212923800-212964200	Weak transcription	HMEC	breast
6	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
8	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
10	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
11	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
12	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
16	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:212952400-212963000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:212952600-212963600	Weak transcription	Colonic Mucosa	Colon
20	chr1:212953000-212964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:212953200-212964400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:212954400-212964400	Weak transcription	Spleen	Spleen
23	chr1:212955000-212964200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:212955200-212963000	Weak transcription	Brain Germinal Matrix	brain
25	chr1:212955600-212964200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:212955800-212964400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:212956400-212963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:212956400-212964200	Weak transcription	NHLF	lung
29	chr1:212956600-212963800	Weak transcription	NHDF-Ad	bronchial
30	chr1:212956600-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:212956600-212964200	Weak transcription	NH-A	brain
32	chr1:212956600-212964200	Weak transcription	Osteobl	bone
33	chr1:212956800-212963600	Weak transcription	A549	lung
34	chr1:212956800-212964200	Weak transcription	Psoas Muscle	Psoas
35	chr1:212957200-212963800	Weak transcription	HUVEC	blood vessel
36	chr1:212957200-212964200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:212957600-212963000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:212957800-212963800	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:212957800-212964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:212958200-212963600	Weak transcription	Fetal Brain Male	brain
41	chr1:212958400-212962800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:212958400-212963600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:212959000-212962800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:212959000-212963600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:212959000-212963800	Weak transcription	Brain Substantia Nigra	brain
46	chr1:212959200-212963800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:212959200-212964200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:212959400-212963800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:212959600-212964200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:212959800-212963600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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