Variant report

Variant	rs1532951
Chromosome Location	chr1:212978197-212978198
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212977806..212980707-chr1:213030715..213033244,2	K562	blood:

Variant related genes	Relation type
ENSG00000198468	Chromatin interaction
ENSG00000162769	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10127512	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127703	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127756	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1046083	0.97[EUR][1000 genomes]
rs10863989	0.94[EUR][1000 genomes]
rs10863997	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120001	0.88[EUR][1000 genomes]
rs11120007	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120014	0.90[GIH][hapmap]
rs11120017	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11120029	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120030	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120035	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11556187	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11800642	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11805669	0.82[EUR][1000 genomes]
rs11806535	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11808846	0.90[GIH][hapmap]
rs11809232	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11809382	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11810895	0.94[EUR][1000 genomes]
rs11811017	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12128410	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12128903	0.95[EUR][1000 genomes]
rs12129933	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12130072	0.81[ASN][1000 genomes]
rs12133124	0.81[AMR][1000 genomes]
rs12137768	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12729663	0.94[EUR][1000 genomes]
rs13376317	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13376383	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13376390	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1507357	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1507358	0.90[GIH][hapmap]
rs17019726	0.93[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271148	0.93[GIH][hapmap]
rs2358899	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34110137	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35213366	0.90[EUR][1000 genomes]
rs3738798	0.90[GIH][hapmap]
rs3738803	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55840547	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56088044	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56243109	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59231663	0.95[EUR][1000 genomes]
rs60308869	0.97[EUR][1000 genomes]
rs6540760	0.97[EUR][1000 genomes]
rs6540762	0.90[GIH][hapmap]
rs6662981	0.94[EUR][1000 genomes]
rs6670648	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6671866	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6681171	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs6687672	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6688238	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6694190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes]
rs6694448	0.97[EUR][1000 genomes]
rs6700204	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6702101	0.90[GIH][hapmap]
rs73081853	0.97[EUR][1000 genomes]
rs73081902	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73083707	0.96[EUR][1000 genomes]
rs73083727	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73083731	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73083749	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73083756	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73083765	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73083778	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7515115	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7516312	1.00[CEU][hapmap];0.96[GIH][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7519582	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7525518	0.94[EUR][1000 genomes]
rs7527216	0.95[EUR][1000 genomes]
rs7536629	0.94[EUR][1000 genomes]
rs7538755	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7546462	0.94[EUR][1000 genomes]
rs7546564	0.94[EUR][1000 genomes]
rs7546754	0.96[EUR][1000 genomes]
rs7548861	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7552880	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7552899	0.81[AMR][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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1532951	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs1532951	TATDN3	cis	Artery Tibial	GTEx
rs1532951	BATF3	cis	cerebellum	SCAN
rs1532951	SNORA16B	cis	cerebellum	SCAN
rs1532951	NCRNA00292	cis	lymphoblastoid	seeQTL
rs1532951	FLVCR1-AS1	cis	Whole Blood	GTEx
rs1532951	FLVCR1	cis	lymphoblastoid	seeQTL
rs1532951	NSL1	cis	parietal	SCAN

Chromatin state (count:114 , 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	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
9	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
10	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
11	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
12	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
14	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
15	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:212967200-212989600	Weak transcription	NHLF	lung
18	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
21	chr1:212968600-212980200	Weak transcription	HUVEC	blood vessel
22	chr1:212969000-212980000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:212969000-212980000	Strong transcription	Dnd41	blood
24	chr1:212969000-212982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:212969000-212982600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:212969000-212983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:212969400-212978600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:212969600-212989000	Weak transcription	HepG2	liver
29	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:212970600-212982800	Weak transcription	Ovary	ovary
31	chr1:212970600-212985200	Weak transcription	Pancreas	Pancrea
32	chr1:212970600-212989600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:212971000-212989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:212971200-212979200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:212971200-212983800	Weak transcription	NH-A	brain
36	chr1:212971200-212990200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:212971400-212987600	Weak transcription	Small Intestine	intestine
38	chr1:212971400-212987800	Weak transcription	A549	lung
39	chr1:212971600-212988000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:212972000-212987800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:212972400-212979200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:212972400-212983000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:212972400-212987800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:212972400-212993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:212972600-212979800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:212972600-212983200	Weak transcription	Gastric	stomach
47	chr1:212972600-212983600	Weak transcription	Fetal Kidney	kidney
48	chr1:212972600-212988000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:212972600-212988000	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr1:212972600-212988000	Weak transcription	Fetal Intestine Small	intestine

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