Variant report

Variant	rs6686164
Chromosome Location	chr1:212963840-212963841
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:212963083-212963971	K562	blood:	n/a	n/a
2	POLR2A	chr1:212963685-212964125	K562	blood:	n/a	n/a
3	HEY1	chr1:212963719-212964208	K562	blood:	n/a	n/a
4	IRF1	chr1:212963788-212963927	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212963280..212966676-chr1:213030010..213031803,4	K562	blood:
2	chr1:212780353..212782606-chr1:212962286..212965026,4	K562	blood:
3	chr1:212963050..212964812-chr1:213052963..213055078,2	K562	blood:
4	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:
5	chr1:212962817..212964825-chr1:212966481..212969163,3	K562	blood:

No data

Variant related genes	Relation type
TATDN3	TF binding region
ENSG00000203705	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000162769	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10127613	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1032962	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1032963	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1032964	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10779583	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10863992	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10864002	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11120005	0.87[EUR][1000 genomes]
rs11120034	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11120038	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12133194	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12239017	0.84[EUR][1000 genomes]
rs12568552	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12744555	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12757944	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1507359	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs15702	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1580991	0.87[EUR][1000 genomes]
rs1580992	0.87[EUR][1000 genomes]
rs1605420	0.83[EUR][1000 genomes]
rs1813705	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1848243	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292214	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2884675	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3738802	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3949369	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4520475	0.83[ASN][1000 genomes]
rs4639827	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951464	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4951639	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6540766	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6540767	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6665489	0.87[EUR][1000 genomes]
rs6670373	0.87[EUR][1000 genomes]
rs6670869	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678961	0.87[EUR][1000 genomes]
rs6681851	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6685864	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6686145	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6689799	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6694887	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696870	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6696908	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6700465	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6702544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703982	0.87[EUR][1000 genomes]
rs7513199	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7513210	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513734	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513772	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514070	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7522100	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528303	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7535608	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7538853	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543603	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547100	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555930	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6686164	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs6686164	FLVCR1-AS1	cis	Whole Blood	GTEx
rs6686164	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs6686164	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs6686164	FLVCR1	Cis_1M	lymphoblastoid	RTeQTL
rs6686164	FLVCR1-AS1	cis	lung	GTEx
rs6686164	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
2	chr1:212895600-212964600	Weak transcription	Gastric	stomach
3	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:212923800-212964200	Weak transcription	HMEC	breast
5	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
7	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
8	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
9	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
13	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:212953000-212964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:212953200-212964400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:212954400-212964400	Weak transcription	Spleen	Spleen
18	chr1:212955000-212964200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:212955600-212964200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:212955800-212964400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:212956400-212964200	Weak transcription	NHLF	lung
22	chr1:212956600-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:212956600-212964200	Weak transcription	NH-A	brain
24	chr1:212956600-212964200	Weak transcription	Osteobl	bone
25	chr1:212956800-212964200	Weak transcription	Psoas Muscle	Psoas
26	chr1:212957200-212964200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:212957800-212964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:212959200-212964200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:212959600-212964200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:212960400-212964200	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:212960400-212964200	Weak transcription	Left Ventricle	heart
32	chr1:212960400-212964200	Weak transcription	Ovary	ovary
33	chr1:212960400-212964400	Weak transcription	Lung	lung
34	chr1:212960400-212964600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:212960600-212964200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:212960600-212964200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:212960600-212964200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:212960600-212964200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:212960600-212964200	Weak transcription	Fetal Kidney	kidney
40	chr1:212960600-212964200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:212960600-212964400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:212961000-212964000	Weak transcription	Fetal Thymus	thymus
43	chr1:212961200-212964200	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr1:212961600-212964000	Weak transcription	Fetal Brain Female	brain
45	chr1:212961600-212964200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:212961600-212964400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr1:212961800-212964200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:212961800-212964400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:212961800-212964400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:212962000-212964400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links