Variant report

Variant	rs4951464
Chromosome Location	chr1:212974356-212974357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212973105..212975746-chr1:212981833..212983410,2	K562	blood:
2	chr1:212963881..212969695-chr1:212970420..212976060,10	K562	blood:
3	chr1:212956561..212959234-chr1:212973278..212975035,2	K562	blood:
4	chr1:212967889..212970692-chr1:212972432..212975770,4	K562	blood:
5	chr1:212973285..212975670-chr1:212976660..212979565,2	K562	blood:

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1021994	0.81[ASN][1000 genomes]
rs1032962	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1032963	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1032965	0.84[ASN][1000 genomes]
rs10779583	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10863992	0.82[AMR][1000 genomes]
rs10864002	0.87[ASN][1000 genomes]
rs11120028	0.90[ASN][1000 genomes]
rs11120034	0.87[ASN][1000 genomes]
rs11120038	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12038225	0.84[ASN][1000 genomes]
rs12124669	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12133194	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12568552	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12744555	0.87[ASN][1000 genomes]
rs12757944	0.87[ASN][1000 genomes]
rs1813705	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1848243	0.80[EUR][1000 genomes]
rs2456818	0.86[ASN][1000 genomes]
rs2456827	0.90[ASN][1000 genomes]
rs2456828	0.82[ASN][1000 genomes]
rs2884675	0.84[ASN][1000 genomes]
rs3738800	0.90[ASN][1000 genomes]
rs3738802	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3949369	0.85[ASN][1000 genomes]
rs4951639	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540766	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6540767	0.87[ASN][1000 genomes]
rs6670869	0.85[AFR][1000 genomes]
rs6681851	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6685864	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6686145	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6686164	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6689799	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6696870	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6696908	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6702544	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7513199	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7513210	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7513734	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7513772	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7514070	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7528303	0.87[ASN][1000 genomes]
rs7543603	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7547100	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7555930	0.83[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4951464	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs4951464	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs4951464	FLVCR1-AS1	cis	lung	GTEx
rs4951464	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs4951464	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs4951464	FLVCR1-AS1	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212965800-212992600	Weak transcription	Lung	lung
2	chr1:212966000-212974800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:212966000-212981200	Weak transcription	Esophagus	oesophagus
4	chr1:212966000-212983000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
6	chr1:212966200-212975600	Weak transcription	HMEC	breast
7	chr1:212966200-212979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:212966400-212977400	Weak transcription	Hela-S3	cervix
9	chr1:212966400-212984000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:212966400-212985600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:212966400-212988200	Weak transcription	Fetal Heart	heart
12	chr1:212966400-212989600	Weak transcription	Fetal Brain Male	brain
13	chr1:212966400-212990200	Weak transcription	Right Ventricle	heart
14	chr1:212966800-212977600	Weak transcription	Brain Germinal Matrix	brain
15	chr1:212966800-212989600	Weak transcription	Psoas Muscle	Psoas
16	chr1:212967000-212979000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:212967000-212984400	Weak transcription	Spleen	Spleen
18	chr1:212967200-212975400	Weak transcription	HSMM	muscle
19	chr1:212967200-212984000	Weak transcription	NHDF-Ad	bronchial
20	chr1:212967200-212988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:212967200-212989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:212967200-212989600	Weak transcription	NHLF	lung
23	chr1:212968000-212980000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:212968000-212987400	Weak transcription	Fetal Intestine Large	intestine
25	chr1:212968400-212974400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:212968400-212988000	Weak transcription	Stomach Mucosa	stomach
27	chr1:212968600-212980200	Weak transcription	HUVEC	blood vessel
28	chr1:212968800-212974600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:212969000-212975400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:212969000-212976200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:212969000-212976400	Strong transcription	Liver	Liver
32	chr1:212969000-212980000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:212969000-212980000	Strong transcription	Dnd41	blood
34	chr1:212969000-212982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:212969000-212982600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:212969000-212983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:212969200-212976200	Strong transcription	Fetal Thymus	thymus
38	chr1:212969400-212978600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:212969600-212989000	Weak transcription	HepG2	liver
40	chr1:212969600-212993000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:212969800-212975000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:212970000-212975600	Strong transcription	Brain Angular Gyrus	brain
43	chr1:212970000-212976200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:212970000-212976200	Strong transcription	Adipose Nuclei	Adipose
45	chr1:212970200-212976200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:212970400-212975800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:212970600-212977600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:212970600-212977800	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:212970600-212982800	Weak transcription	Ovary	ovary
50	chr1:212970600-212985200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links