Variant report

Variant	rs6669492
Chromosome Location	chr1:212916748-212916749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10494955	0.88[ASN][1000 genomes]
rs10863990	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863993	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10863995	0.84[ASN][1000 genomes]
rs10863998	0.89[ASN][1000 genomes]
rs10863999	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864000	0.80[ASN][1000 genomes]
rs10864001	0.80[ASN][1000 genomes]
rs11120002	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11120011	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120012	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120013	0.92[ASN][1000 genomes]
rs11120019	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120024	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120025	0.87[AFR][1000 genomes]
rs11120026	0.85[ASN][1000 genomes]
rs11120027	0.85[ASN][1000 genomes]
rs1133462	0.80[ASN][1000 genomes]
rs12064985	0.83[ASN][1000 genomes]
rs12088916	0.90[ASN][1000 genomes]
rs12097897	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12125321	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12126017	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12130945	0.80[ASN][1000 genomes]
rs12132316	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12136046	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12136834	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12722742	0.90[ASN][1000 genomes]
rs12725274	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12727790	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12737398	0.80[ASN][1000 genomes]
rs12741704	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12743402	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12747251	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12758602	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12759287	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2359322	0.80[ASN][1000 genomes]
rs34274815	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3820679	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3862953	0.80[ASN][1000 genomes]
rs4951463	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4951636	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4951637	0.86[AFR][1000 genomes]
rs4951638	0.92[ASN][1000 genomes]
rs61829227	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6540761	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6540763	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6661720	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6679350	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6679549	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6690689	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693311	0.90[ASN][1000 genomes]
rs6694452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702025	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6702611	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7554105	0.80[ASN][1000 genomes]
rs7556272	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6669492	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895200-212922800	Weak transcription	Left Ventricle	heart
2	chr1:212895400-212917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:212895400-212923200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:212895400-212923400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:212895400-212923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
7	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
8	chr1:212895600-212923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:212895600-212923400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:212895600-212964600	Weak transcription	Gastric	stomach
11	chr1:212895800-212917400	Weak transcription	NHLF	lung
12	chr1:212895800-212925600	Weak transcription	Small Intestine	intestine
13	chr1:212895800-212926200	Weak transcription	Hela-S3	cervix
14	chr1:212896000-212917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:212896400-212917000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:212898600-212923200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:212898800-212934000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:212899800-212926400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:212900400-212917400	Weak transcription	Fetal Stomach	stomach
20	chr1:212900400-212923200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:212900400-212927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:212900400-212932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:212900400-212936200	Weak transcription	Aorta	Aorta
24	chr1:212901400-212954000	Weak transcription	NH-A	brain
25	chr1:212901600-212923000	Weak transcription	HSMM	muscle
26	chr1:212902200-212941800	Weak transcription	Fetal Kidney	kidney
27	chr1:212902600-212943600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:212902800-212917200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:212902800-212917200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:212903000-212923400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:212903200-212918000	Weak transcription	Fetal Intestine Large	intestine
32	chr1:212903200-212923400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:212903600-212926400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:212904200-212923200	Weak transcription	Adipose Nuclei	Adipose
35	chr1:212904800-212926200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:212905200-212923200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:212905200-212923400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:212905600-212923400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:212906200-212923400	Weak transcription	HMEC	breast
40	chr1:212906800-212923400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:212907000-212917000	Weak transcription	Thymus	Thymus
42	chr1:212907800-212917000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:212908000-212933200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:212909400-212923200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:212911000-212922800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:212911400-212917000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr1:212911600-212923000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:212911800-212918600	Weak transcription	Fetal Lung	lung
49	chr1:212912000-212923200	Weak transcription	Liver	Liver
50	chr1:212912000-212935800	Weak transcription	K562	blood

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