Variant report

Variant	rs3820679
Chromosome Location	chr1:212961143-212961144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212781016..212783376-chr1:212959692..212961449,2	MCF-7	breast:
2	chr1:212960294..212962883-chr1:213188555..213191323,2	K562	blood:
3	chr1:212955485..212957431-chr1:212958159..212961189,3	K562	blood:
4	chr1:212960922..212962804-chr1:212968235..212970840,2	K562	blood:
5	chr1:212958137..212960134-chr1:212960164..212962206,2	K562	blood:
6	chr1:212949377..212951315-chr1:212960542..212962942,2	K562	blood:
7	chr1:212958789..212962181-chr1:212964353..212966610,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203705	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000174606	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10494955	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1054733	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10863990	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10863993	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10863995	0.87[ASN][1000 genomes]
rs10863998	0.95[ASN][1000 genomes]
rs10863999	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10864001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120002	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11120011	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11120012	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120013	0.92[ASN][1000 genomes]
rs11120019	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11120024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11120025	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120026	0.99[ASN][1000 genomes]
rs11120027	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs11120032	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11120037	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120039	0.85[ASN][1000 genomes]
rs1133462	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12064985	0.98[ASN][1000 genomes]
rs12088916	0.93[ASN][1000 genomes]
rs12095846	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12097897	0.84[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12125321	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12126017	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12130945	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12132316	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12136046	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136834	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12722742	0.93[ASN][1000 genomes]
rs12725274	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12727790	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12734406	0.81[ASN][1000 genomes]
rs12734543	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12737398	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12741704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743402	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12744602	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12747251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12758602	0.84[AFR][1000 genomes]
rs12759287	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2359322	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34274815	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3862953	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951457	0.86[YRI][hapmap]
rs4951463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951636	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4951637	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4951638	0.92[ASN][1000 genomes]
rs61829227	0.82[AFR][1000 genomes]
rs61829243	0.88[ASN][1000 genomes]
rs6540761	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6540763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6661720	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669492	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6679350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6689604	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6690689	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693311	0.93[ASN][1000 genomes]
rs6694452	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697507	0.86[ASN][1000 genomes]
rs6700410	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs6702025	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6702611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554105	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556272	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3820679	NSL1	Cis_1M	lymphoblastoid	RTeQTL
rs3820679	LQK1	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:212923600-212963800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:212923600-212964400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:212923800-212964200	Weak transcription	HMEC	breast
6	chr1:212926600-212963400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:212927400-212963400	Weak transcription	Small Intestine	intestine
8	chr1:212927400-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:212936600-212964400	Weak transcription	Esophagus	oesophagus
10	chr1:212941200-212964200	Weak transcription	Right Ventricle	heart
11	chr1:212942400-212964200	Weak transcription	Aorta	Aorta
12	chr1:212942600-212964400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:212942800-212964200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:212943200-212964200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:212944200-212964400	Weak transcription	Fetal Heart	heart
16	chr1:212950400-212964200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:212951800-212964400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:212952400-212963000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:212952600-212963600	Weak transcription	Colonic Mucosa	Colon
20	chr1:212953000-212964400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:212953200-212964400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:212954000-212961200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:212954000-212961200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:212954200-212961600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:212954400-212964400	Weak transcription	Spleen	Spleen
26	chr1:212955000-212961400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:212955000-212961600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:212955000-212962000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:212955000-212964200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:212955200-212961600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:212955200-212963000	Weak transcription	Brain Germinal Matrix	brain
32	chr1:212955600-212961800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:212955600-212964200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:212955800-212964400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:212956000-212961800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:212956400-212962000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:212956400-212963000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:212956400-212964200	Weak transcription	NHLF	lung
39	chr1:212956600-212962000	Weak transcription	GM12878-XiMat	blood
40	chr1:212956600-212963800	Weak transcription	NHDF-Ad	bronchial
41	chr1:212956600-212964200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:212956600-212964200	Weak transcription	NH-A	brain
43	chr1:212956600-212964200	Weak transcription	Osteobl	bone
44	chr1:212956800-212963600	Weak transcription	A549	lung
45	chr1:212956800-212964200	Weak transcription	Psoas Muscle	Psoas
46	chr1:212957200-212961200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr1:212957200-212963800	Weak transcription	HUVEC	blood vessel
48	chr1:212957200-212964200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:212957600-212961800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:212957600-212963000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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