Variant report

Variant	rs3008637
Chromosome Location	chr1:222857769-222857770
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222852029..222855795-chr1:222856655..222859016,3	K562	blood:
2	chr1:222847814..222850945-chr1:222855143..222857892,3	K562	blood:

Variant related genes	Relation type
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11485123	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063226	0.86[EUR][1000 genomes]
rs1391557	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1391558	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1498382	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17011686	0.95[ASN][1000 genomes]
rs17163450	0.92[ASN][1000 genomes]
rs17163468	0.92[ASN][1000 genomes]
rs1909197	0.81[EUR][1000 genomes]
rs2030076	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088514	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2133188	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2270707	0.81[EUR][1000 genomes]
rs2378604	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2936020	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936023	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936051	0.90[EUR][1000 genomes]
rs2936052	0.90[EUR][1000 genomes]
rs2936054	0.89[EUR][1000 genomes]
rs3002129	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3002146	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3002148	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008614	0.89[EUR][1000 genomes]
rs3008615	0.89[EUR][1000 genomes]
rs3008616	0.89[EUR][1000 genomes]
rs3008618	0.91[EUR][1000 genomes]
rs3008622	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3008625	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008629	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34433664	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35507977	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3811465	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61824336	0.82[AFR][1000 genomes]
rs61827168	0.90[EUR][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	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
2	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
3	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
4	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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222839000-222859800	Weak transcription	Small Intestine	intestine
3	chr1:222839000-222877400	Weak transcription	Psoas Muscle	Psoas
4	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:222839200-222861200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
7	chr1:222839800-222859600	Weak transcription	Brain Angular Gyrus	brain
8	chr1:222839800-222859600	Weak transcription	Fetal Brain Male	brain
9	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
10	chr1:222841000-222859600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:222841200-222866200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:222841200-222883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:222841400-222883200	Weak transcription	Fetal Heart	heart
14	chr1:222842800-222867800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:222843400-222860200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:222844000-222863600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:222845000-222859600	Weak transcription	Spleen	Spleen
18	chr1:222845000-222866800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:222845000-222884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:222845200-222859600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:222845200-222859600	Weak transcription	Hela-S3	cervix
22	chr1:222845200-222864400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:222845400-222859400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:222845600-222859600	Weak transcription	Fetal Kidney	kidney
25	chr1:222846200-222858400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:222846200-222859000	Weak transcription	Thymus	Thymus
27	chr1:222846200-222859200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:222846200-222859400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:222846200-222859400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:222846200-222859400	Weak transcription	GM12878-XiMat	blood
31	chr1:222846200-222859600	Weak transcription	Aorta	Aorta
32	chr1:222846400-222858200	Weak transcription	Fetal Lung	lung
33	chr1:222846400-222858400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:222846400-222859400	Weak transcription	Brain Substantia Nigra	brain
35	chr1:222846400-222859400	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:222846400-222859400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:222846600-222859600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:222847600-222859600	Weak transcription	HepG2	liver
39	chr1:222847800-222859600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:222847800-222872000	Weak transcription	Fetal Intestine Small	intestine
41	chr1:222848800-222859600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:222849000-222858200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:222849200-222858400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr1:222849200-222859600	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:222849200-222859800	Weak transcription	A549	lung
46	chr1:222849200-222862400	Weak transcription	Right Ventricle	heart
47	chr1:222849200-222875600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:222849400-222858200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:222849400-222858400	Weak transcription	Brain Germinal Matrix	brain
50	chr1:222849400-222858600	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links