Variant report

Variant	rs3850855
Chromosome Location	chr1:45523893-45523894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45521218..45524154-chr1:45525277..45526789,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10789454	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11211074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1144868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11806438	0.98[ASN][1000 genomes]
rs11810239	0.97[ASN][1000 genomes]
rs1226670	0.98[ASN][1000 genomes]
rs1226733	0.97[ASN][1000 genomes]
rs1226734	0.97[ASN][1000 genomes]
rs1226735	0.82[ASN][1000 genomes]
rs1226746	0.98[ASN][1000 genomes]
rs1226747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1226748	0.98[ASN][1000 genomes]
rs1226836	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1226914	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1612575	1.00[CHD][hapmap]
rs1782459	0.95[ASN][1000 genomes]
rs1938300	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938303	0.98[ASN][1000 genomes]
rs1938304	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1938407	0.82[EUR][1000 genomes]
rs2088956	1.00[ASN][1000 genomes]
rs2105458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2186219	0.82[EUR][1000 genomes]
rs2202152	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2228084	0.90[CHD][hapmap]
rs2356302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs238249	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997458	0.81[EUR][1000 genomes]
rs2997461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3009968	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3009969	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3009974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3009979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3121732	1.00[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs3121769	0.82[EUR][1000 genomes]
rs34134455	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346684	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346687	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346693	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346695	0.98[ASN][1000 genomes]
rs346696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346697	0.98[ASN][1000 genomes]
rs346698	0.98[ASN][1000 genomes]
rs346700	0.98[ASN][1000 genomes]
rs346701	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346702	0.98[ASN][1000 genomes]
rs346703	1.00[CHD][hapmap]
rs346705	0.98[ASN][1000 genomes]
rs346706	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346707	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346708	0.91[ASN][1000 genomes]
rs346712	0.98[ASN][1000 genomes]
rs346716	0.98[ASN][1000 genomes]
rs346717	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346721	0.98[ASN][1000 genomes]
rs346723	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346725	1.00[CHD][hapmap]
rs346729	0.98[ASN][1000 genomes]
rs346731	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346732	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs346733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346734	0.98[ASN][1000 genomes]
rs346735	0.98[ASN][1000 genomes]
rs346736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346737	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs365108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3738246	1.00[ASN][1000 genomes]
rs3850856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs415536	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4454584	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs454624	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4660295	0.98[ASN][1000 genomes]
rs4660834	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4660839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4660841	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4660842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56363452	0.98[ASN][1000 genomes]
rs56791336	0.98[ASN][1000 genomes]
rs58374842	0.98[ASN][1000 genomes]
rs58934647	0.98[ASN][1000 genomes]
rs59220391	0.88[ASN][1000 genomes]
rs61789780	0.98[ASN][1000 genomes]
rs61789781	0.98[ASN][1000 genomes]
rs6429557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688318	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6702327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs72684493	0.98[ASN][1000 genomes]
rs974143	0.98[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	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	nsv546148	chr1:45500294-45627663	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45481200-45525000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:45481200-45527400	Weak transcription	Left Ventricle	heart
3	chr1:45497400-45525400	Weak transcription	Gastric	stomach
4	chr1:45498000-45525600	Weak transcription	Pancreas	Pancrea
5	chr1:45501800-45527000	Weak transcription	Fetal Brain Male	brain
6	chr1:45504200-45524200	Weak transcription	Esophagus	oesophagus
7	chr1:45504400-45524000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:45505000-45526000	Weak transcription	Fetal Stomach	stomach
9	chr1:45507600-45527000	Weak transcription	Fetal Kidney	kidney
10	chr1:45509000-45524000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:45509600-45526200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:45513600-45525400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:45513600-45526200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:45517000-45525600	Weak transcription	Small Intestine	intestine
15	chr1:45517400-45526200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:45517600-45526800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:45517800-45525600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr1:45520400-45529200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:45521200-45525800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:45521200-45525800	Strong transcription	HepG2	liver
21	chr1:45521200-45526600	Strong transcription	Ovary	ovary
22	chr1:45521400-45525800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:45521400-45526000	Strong transcription	Brain Germinal Matrix	brain
24	chr1:45521400-45527400	Weak transcription	Fetal Intestine Small	intestine
25	chr1:45522200-45524800	Strong transcription	Brain Anterior Caudate	brain
26	chr1:45522400-45524800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr1:45522600-45524600	Strong transcription	Brain Substantia Nigra	brain
28	chr1:45522600-45524600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:45522600-45525800	Strong transcription	Brain Hippocampus Middle	brain
30	chr1:45522600-45526000	Strong transcription	Fetal Brain Female	brain
31	chr1:45522800-45524400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:45523000-45524600	Strong transcription	Aorta	Aorta
33	chr1:45523000-45525200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:45523000-45525200	Strong transcription	Brain Angular Gyrus	brain
35	chr1:45523000-45525400	Weak transcription	Adipose Nuclei	Adipose
36	chr1:45523400-45527400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:45523600-45526200	Weak transcription	Colonic Mucosa	Colon
38	chr1:45523600-45526600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:45523600-45527400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:45523800-45524600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:45523800-45524800	Strong transcription	Fetal Intestine Large	intestine
42	chr1:45523800-45525800	Strong transcription	Brain Cingulate Gyrus	brain
43	chr1:45523800-45525800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr1:45523800-45526000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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