Variant report

Variant	rs6674786
Chromosome Location	chr1:213066460-213066461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10779596	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10864024	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10864030	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12074192	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12405742	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12408694	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1390501	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2359323	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2359326	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6674782	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6682947	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6683314	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][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	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6674786	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213032600-213073000	Weak transcription	Colonic Mucosa	Colon
2	chr1:213032600-213073000	Weak transcription	Esophagus	oesophagus
3	chr1:213034400-213068000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:213034600-213067800	Weak transcription	NHLF	lung
5	chr1:213034600-213070600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:213035800-213073000	Weak transcription	Small Intestine	intestine
7	chr1:213036000-213070800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:213037600-213073200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:213038400-213072000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:213039600-213073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:213040400-213073000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:213043200-213073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:213045000-213070800	Weak transcription	Pancreas	Pancrea
14	chr1:213047000-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:213049000-213073000	Weak transcription	HSMMtube	muscle
16	chr1:213049800-213072400	Weak transcription	Fetal Brain Male	brain
17	chr1:213049800-213073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:213049800-213073200	Weak transcription	Spleen	Spleen
19	chr1:213052200-213073000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:213052800-213073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:213053400-213073800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:213053600-213073000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:213053800-213073200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:213053800-213073200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:213054000-213071000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:213054200-213071400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:213054400-213073200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:213055000-213073600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:213055200-213073200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr1:213055800-213066600	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr1:213056000-213071200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:213056000-213072200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:213056200-213072000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:213056200-213074200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:213056400-213068000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr1:213056400-213070000	Strong transcription	K562	blood
37	chr1:213056400-213073400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:213056600-213066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:213056600-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:213056800-213073000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:213057000-213068400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:213057000-213072200	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:213057000-213073400	Strong transcription	Fetal Intestine Large	intestine
44	chr1:213057600-213067800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:213057600-213075000	Weak transcription	Right Ventricle	heart
46	chr1:213058000-213073400	Strong transcription	A549	lung
47	chr1:213058600-213073000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:213059400-213073600	Strong transcription	Primary T cells from cord blood	blood
49	chr1:213060400-213072800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:213061800-213068000	Strong transcription	Brain Hippocampus Middle	brain

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