Variant report

Variant	rs1284856
Chromosome Location	chr1:213071210-213071211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:213067051..213070397-chr1:213070483..213072909,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10864023	0.98[ASN][1000 genomes]
rs10864028	0.91[ASN][1000 genomes]
rs10864029	0.90[ASN][1000 genomes]
rs11120062	0.97[ASN][1000 genomes]
rs11582817	0.91[ASN][1000 genomes]
rs11586464	0.85[ASN][1000 genomes]
rs12036853	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12136547	0.95[ASN][1000 genomes]
rs12404754	0.98[ASN][1000 genomes]
rs12405293	0.98[ASN][1000 genomes]
rs12567976	0.98[ASN][1000 genomes]
rs12754609	0.98[ASN][1000 genomes]
rs12755947	0.98[ASN][1000 genomes]
rs1284852	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1284854	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1284855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1587175	0.98[ASN][1000 genomes]
rs2359325	0.98[ASN][1000 genomes]
rs3207090	0.98[ASN][1000 genomes]
rs4951471	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670064	0.91[ASN][1000 genomes]
rs6702876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541559	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1284856	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs1284856	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs1284856	FLVCR1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 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	chr1:213035800-213073000	Weak transcription	Small Intestine	intestine
4	chr1:213037600-213073200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:213038400-213072000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:213039600-213073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:213040400-213073000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:213043200-213073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:213047000-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:213049000-213073000	Weak transcription	HSMMtube	muscle
11	chr1:213049800-213072400	Weak transcription	Fetal Brain Male	brain
12	chr1:213049800-213073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:213049800-213073200	Weak transcription	Spleen	Spleen
14	chr1:213052200-213073000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:213052800-213073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:213053400-213073800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:213053600-213073000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:213053800-213073200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:213053800-213073200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:213054200-213071400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:213054400-213073200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:213055000-213073600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:213055200-213073200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:213056000-213072200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:213056200-213072000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:213056200-213074200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:213056400-213073400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:213056600-213073600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:213056800-213073000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:213057000-213072200	Strong transcription	Fetal Muscle Leg	muscle
31	chr1:213057000-213073400	Strong transcription	Fetal Intestine Large	intestine
32	chr1:213057600-213075000	Weak transcription	Right Ventricle	heart
33	chr1:213058000-213073400	Strong transcription	A549	lung
34	chr1:213058600-213073000	Weak transcription	Brain Germinal Matrix	brain
35	chr1:213059400-213073600	Strong transcription	Primary T cells from cord blood	blood
36	chr1:213060400-213072800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:213061800-213071600	Strong transcription	Left Ventricle	heart
38	chr1:213062400-213073400	Weak transcription	Psoas Muscle	Psoas
39	chr1:213062600-213075000	Weak transcription	Thymus	Thymus
40	chr1:213063400-213072000	Weak transcription	Brain Angular Gyrus	brain
41	chr1:213063600-213074800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:213063800-213073200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:213064000-213073000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:213064400-213073000	Weak transcription	NHEK	skin
45	chr1:213064400-213073200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr1:213064400-213073200	Weak transcription	NHDF-Ad	bronchial
47	chr1:213065400-213073800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:213065800-213073000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:213065800-213073200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:213066400-213072000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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