Variant report

Variant	rs2006790
Chromosome Location	chr1:222761284-222761285
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222759001..222761767-chr1:222763501..222765317,2	MCF-7	breast:
2	chr1:222753738..222756100-chr1:222759051..222761719,2	MCF-7	breast:
3	chr1:222760074..222764679-chr1:222790714..222794830,7	K562	blood:
4	chr1:222760324..222764721-chr1:222884429..222887789,6	K562	blood:
5	chr1:222761198..222763394-chr1:222816241..222819069,2	K562	blood:
6	chr1:222760324..222762063-chr1:222884419..222886498,2	K562	blood:
7	chr1:222760723..222765796-chr1:222790714..222795393,9	K562	blood:

Variant related genes	Relation type
ENSG00000186063	Chromatin interaction
ENSG00000162819	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1024065	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495194	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17463740	0.91[EUR][1000 genomes]
rs17464857	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17511318	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1909194	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1982983	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2936030	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936044	0.87[EUR][1000 genomes]
rs2936045	0.87[EUR][1000 genomes]
rs2936046	0.87[EUR][1000 genomes]
rs3002130	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3008645	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3008647	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3008654	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3008655	0.85[EUR][1000 genomes]
rs35750438	0.91[EUR][1000 genomes]
rs3748625	0.97[ASN][1000 genomes]
rs3828060	0.97[ASN][1000 genomes]
rs4328077	0.89[EUR][1000 genomes]
rs73122816	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73122823	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122834	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122837	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122849	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122850	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122857	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74145503	0.94[AMR][1000 genomes]
rs74148133	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74148140	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74148142	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9441828	0.87[EUR][1000 genomes]
rs9441911	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1842070	chr1:222732027-222763235	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222721200-222762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222721800-222762400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:222725600-222762200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:222727600-222762600	Weak transcription	Aorta	Aorta
5	chr1:222727800-222762400	Weak transcription	Thymus	Thymus
6	chr1:222728200-222762200	Weak transcription	Small Intestine	intestine
7	chr1:222729600-222762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:222731200-222762400	Weak transcription	Spleen	Spleen
9	chr1:222731600-222762200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:222733600-222762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:222733800-222761800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:222733800-222762200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:222734000-222762400	Weak transcription	Right Ventricle	heart
14	chr1:222734200-222762400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:222734800-222762200	Weak transcription	Colonic Mucosa	Colon
16	chr1:222739000-222761600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:222742200-222762400	Weak transcription	Fetal Kidney	kidney
18	chr1:222742800-222762200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:222743000-222762400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:222743400-222761600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:222743600-222762200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:222745800-222762200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:222746000-222762600	Weak transcription	Lung	lung
24	chr1:222746600-222761800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:222750400-222762000	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:222751000-222761600	Weak transcription	Brain Germinal Matrix	brain
27	chr1:222751000-222762600	Weak transcription	Left Ventricle	heart
28	chr1:222751600-222762200	Weak transcription	Fetal Heart	heart
29	chr1:222754600-222761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:222754800-222761400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:222754800-222761600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:222754800-222761800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:222756000-222761800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:222756000-222762200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:222756000-222762200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:222756200-222761800	Weak transcription	NHLF	lung
37	chr1:222756200-222762200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:222756400-222762200	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:222756400-222762200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:222756400-222762400	Weak transcription	Esophagus	oesophagus
41	chr1:222756600-222761600	Weak transcription	Hela-S3	cervix
42	chr1:222756600-222762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:222756800-222761400	Weak transcription	Brain Anterior Caudate	brain
44	chr1:222756800-222761600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr1:222757000-222762000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:222757000-222762400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:222757000-222762400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:222757200-222762200	Weak transcription	Fetal Intestine Small	intestine
49	chr1:222757200-222762200	Weak transcription	Fetal Stomach	stomach
50	chr1:222757200-222762200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links