Variant report

Variant	rs12565557
Chromosome Location	chr1:212980368-212980369
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	chr1:212976311..212977926-chr1:212979767..212982509,2	K562	blood:
2	chr1:212977806..212980707-chr1:213030715..213033244,2	K562	blood:

Variant related genes	Relation type
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10494955	0.83[ASN][1000 genomes]
rs1054733	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10863998	0.81[ASN][1000 genomes]
rs10863999	0.82[ASN][1000 genomes]
rs10864000	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10864001	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120024	0.81[ASN][1000 genomes]
rs11120032	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120037	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120039	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1133462	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12095846	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12097897	0.82[ASN][1000 genomes]
rs12126017	0.82[ASN][1000 genomes]
rs12130945	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12734406	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12734543	0.90[ASN][1000 genomes]
rs12737398	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12744602	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2359322	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862953	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6689604	0.85[ASN][1000 genomes]
rs6697507	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6700410	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6702611	0.82[ASN][1000 genomes]
rs7554105	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[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	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
2	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
3	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
4	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
5	esv3451953	chr1:212979379-212981477	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12565557	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs12565557	LQK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
3	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
5	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
8	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
9	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
10	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
11	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
12	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
13	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:212967200-212989600	Weak transcription	NHLF	lung
16	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
17	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
18	chr1:212969000-212982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:212969000-212982600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:212969000-212983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:212969600-212989000	Weak transcription	HepG2	liver
22	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:212970600-212982800	Weak transcription	Ovary	ovary
24	chr1:212970600-212985200	Weak transcription	Pancreas	Pancrea
25	chr1:212970600-212989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:212971000-212989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:212971200-212983800	Weak transcription	NH-A	brain
28	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:212971400-212987600	Weak transcription	Small Intestine	intestine
30	chr1:212971400-212987800	Weak transcription	A549	lung
31	chr1:212971600-212988000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr1:212972000-212987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:212972400-212983000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:212972400-212987800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:212972600-212983200	Weak transcription	Gastric	stomach
37	chr1:212972600-212983600	Weak transcription	Fetal Kidney	kidney
38	chr1:212972600-212988000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:212972600-212988000	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:212972600-212988000	Weak transcription	Fetal Intestine Small	intestine
41	chr1:212972600-212989800	Weak transcription	HSMMtube	muscle
42	chr1:212972600-212990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:212973000-212988600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:212973400-212981000	Weak transcription	GM12878-XiMat	blood
45	chr1:212973600-212982800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:212973800-212982800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:212974600-212980400	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:212974600-212981000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr1:212975000-212980400	Weak transcription	Left Ventricle	heart
50	chr1:212975400-212981800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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