Variant report

Variant	rs2294292
Chromosome Location	chr1:171482686-171482687
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:171482500..171484395-chr1:171486369..171488857,2	K562	blood:
2	chr1:171480931..171484938-chr1:171487047..171489440,3	MCF-7	breast:
3	chr1:171476248..171479748-chr1:171482542..171484607,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000201126	Chromatin interaction
ENSG00000117523	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1055417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913167	1.00[CHB][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119596	0.90[ASN][1000 genomes]
rs12129856	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131694	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136576	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12137832	1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12139715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12142594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145045	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12145085	0.86[EUR][1000 genomes]
rs12146022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12733939	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12734261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12759907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171005	0.84[EUR][1000 genomes]
rs183533	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs190198	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2294293	1.00[CEU][hapmap];1.00[CHB][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]
rs235471	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235472	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235477	0.83[EUR][1000 genomes]
rs235488	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235498	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235507	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235886	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs235892	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs235893	0.84[EUR][1000 genomes]
rs235895	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs235897	0.84[EUR][1000 genomes]
rs235898	0.83[EUR][1000 genomes]
rs235899	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235900	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235901	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235902	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235903	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs235904	0.81[EUR][1000 genomes]
rs235910	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs235911	0.86[EUR][1000 genomes]
rs235912	0.94[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs46407	0.81[EUR][1000 genomes]
rs56207586	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591286	0.84[EUR][1000 genomes]
rs67133611	0.81[EUR][1000 genomes]
rs71637410	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71637418	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71637419	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74122850	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7534557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7538745	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
2	chr1:171463000-171483200	Weak transcription	Fetal Muscle Leg	muscle
3	chr1:171464000-171483200	Weak transcription	Esophagus	oesophagus
4	chr1:171465200-171483200	Weak transcription	NHLF	lung
5	chr1:171465200-171483600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:171468400-171483200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:171468800-171483600	Weak transcription	Gastric	stomach
8	chr1:171469000-171483600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:171470200-171482800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:171470600-171483600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:171470600-171491600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:171471400-171483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:171471400-171485800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:171471600-171483200	Weak transcription	Fetal Brain Female	brain
15	chr1:171471600-171483600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:171471600-171483600	Weak transcription	Fetal Brain Male	brain
17	chr1:171472000-171483800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:171472400-171483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:171472400-171483600	Weak transcription	Aorta	Aorta
20	chr1:171472600-171483200	Weak transcription	Lung	lung
21	chr1:171472600-171483800	Weak transcription	Fetal Stomach	stomach
22	chr1:171473200-171486400	Weak transcription	Pancreas	Pancrea
23	chr1:171475400-171483200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr1:171475400-171483600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:171475400-171484000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:171475400-171486200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:171475800-171484400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:171475800-171486400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:171475800-171524400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:171476000-171483600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr1:171476000-171498800	Weak transcription	Fetal Heart	heart
32	chr1:171476200-171483200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:171476200-171483600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:171476200-171486600	Weak transcription	Brain Substantia Nigra	brain
35	chr1:171476400-171483200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:171476400-171483200	Weak transcription	Thymus	Thymus
37	chr1:171476400-171483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:171476600-171483600	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:171476600-171483600	Weak transcription	Left Ventricle	heart
40	chr1:171476600-171489000	Weak transcription	Right Ventricle	heart
41	chr1:171476800-171483600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:171476800-171483600	Weak transcription	Psoas Muscle	Psoas
43	chr1:171476800-171483600	Weak transcription	Spleen	Spleen
44	chr1:171477000-171483200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:171477000-171483600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:171477200-171483600	Weak transcription	Colonic Mucosa	Colon
47	chr1:171477400-171484000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:171477400-171486600	Weak transcription	Brain Angular Gyrus	brain
49	chr1:171477600-171483200	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:171477600-171486400	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links