Variant report

Variant	rs6700204
Chromosome Location	chr1:212944966-212944967
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10127512	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10127703	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10127756	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1046083	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863989	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863997	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120001	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11120007	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11120010	0.81[ASN][1000 genomes]
rs11120014	0.81[ASN][1000 genomes]
rs11120017	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120018	0.83[ASN][1000 genomes]
rs11120029	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11120030	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11556187	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11800642	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11806535	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11808846	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11809232	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11809382	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11810895	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11811017	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12119531	0.83[ASN][1000 genomes]
rs12128410	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12128903	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12129465	0.81[ASN][1000 genomes]
rs12133174	0.81[ASN][1000 genomes]
rs12137768	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139618	0.83[ASN][1000 genomes]
rs12145131	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12402370	0.97[ASN][1000 genomes]
rs12404618	0.81[ASN][1000 genomes]
rs12404885	0.81[ASN][1000 genomes]
rs12406499	0.81[ASN][1000 genomes]
rs12729663	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13376317	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13376383	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13376390	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1507357	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1507358	0.81[ASN][1000 genomes]
rs1532951	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17019726	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1857971	0.81[ASN][1000 genomes]
rs2174780	0.89[ASN][1000 genomes]
rs2271148	0.89[ASN][1000 genomes]
rs2358899	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34110137	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35213366	0.89[EUR][1000 genomes]
rs3738798	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3738803	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55840547	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56088044	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56243109	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57449384	0.97[ASN][1000 genomes]
rs58203936	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59231663	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60308869	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61736926	0.83[ASN][1000 genomes]
rs6540760	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6540762	0.81[ASN][1000 genomes]
rs6657089	0.86[ASN][1000 genomes]
rs6662981	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6670648	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671866	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681171	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6687672	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6688238	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6694448	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73081853	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73081902	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73083705	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73083707	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73083727	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73083731	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73083743	0.94[ASN][1000 genomes]
rs73083749	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73083756	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73083765	0.93[EUR][1000 genomes]
rs7516312	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7519582	0.93[EUR][1000 genomes]
rs7525518	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7527216	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7536629	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7538755	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7546462	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7546564	0.93[EUR][1000 genomes]
rs7546754	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7548861	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7552880	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	nsv1005983	chr1:212917531-212947521	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6700204	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 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	chr1:212923800-212947200	Weak transcription	A549	lung
8	chr1:212923800-212957600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:212923800-212964200	Weak transcription	HMEC	breast
10	chr1:212924000-212954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:212926600-212954200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:212926800-212947800	Weak transcription	NHDF-Ad	bronchial
14	chr1:212926800-212948000	Weak transcription	Osteobl	bone
15	chr1:212926800-212954200	Weak transcription	Hela-S3	cervix
16	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
17	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:212928400-212954000	Weak transcription	Fetal Brain Male	brain
19	chr1:212928400-212956200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:212928600-212947800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:212928600-212954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:212929000-212947800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:212934200-212952400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:212936600-212950600	Weak transcription	Placenta	Placenta
25	chr1:212936600-212954800	Weak transcription	Left Ventricle	heart
26	chr1:212936600-212956000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:212936600-212956200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:212936600-212956200	Weak transcription	Thymus	Thymus
29	chr1:212936600-212959800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:212936600-212960200	Weak transcription	Lung	lung
31	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
32	chr1:212938800-212946400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:212938800-212946600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:212939400-212956200	Weak transcription	Fetal Stomach	stomach
35	chr1:212939600-212946200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:212940000-212945600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
38	chr1:212941600-212945600	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr1:212941600-212945600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr1:212941600-212945600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr1:212941800-212945800	ZNF genes & repeats	GM12878-XiMat	blood
42	chr1:212942400-212945200	Weak transcription	Ovary	ovary
43	chr1:212942400-212945600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:212942400-212950400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
46	chr1:212942600-212946400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:212942800-212956400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:212943000-212954200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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