Variant report

Variant	rs11577641
Chromosome Location	chr1:169858192-169858193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10489175	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10800488	0.88[EUR][1000 genomes]
rs11578817	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11579102	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11579254	1.00[CEU][hapmap]
rs11579709	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11581959	0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11582552	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11584208	1.00[CEU][hapmap]
rs11585093	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11588736	1.00[CEU][hapmap]
rs11589659	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11589671	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11590604	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1360294	0.88[CEU][hapmap]
rs1572551	1.00[CEU][hapmap]
rs16828209	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16862683	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16862705	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16862902	1.00[CEU][hapmap]
rs1928887	1.00[CEU][hapmap]
rs2420510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2420511	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34657513	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35196850	0.91[EUR][1000 genomes]
rs3753312	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766139	0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766146	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766150	1.00[ASW][hapmap];0.88[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3817859	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs41496844	1.00[CEU][hapmap]
rs4656198	0.89[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.82[MEX][hapmap]
rs4656201	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656202	1.00[CEU][hapmap]
rs4656718	0.89[ASW][hapmap]
rs4656720	0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4656722	0.93[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4656723	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4656726	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4656727	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4656732	1.00[CEU][hapmap]
rs55806711	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57805301	0.89[EUR][1000 genomes]
rs58111285	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60191157	0.89[EUR][1000 genomes]
rs60315765	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61806076	0.88[EUR][1000 genomes]
rs61807812	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61807813	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61807814	0.85[EUR][1000 genomes]
rs61807817	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61807818	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61807835	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61807840	0.91[EUR][1000 genomes]
rs6685211	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73026253	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
3	chr1:169833800-169860200	Weak transcription	HMEC	breast
4	chr1:169842400-169860000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:169844000-169860000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:169844800-169860600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
8	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:169845400-169859600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:169845400-169860000	Weak transcription	Psoas Muscle	Psoas
11	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:169847000-169859000	Weak transcription	Left Ventricle	heart
13	chr1:169847200-169860000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:169847200-169860000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:169847400-169860000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:169848000-169859000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:169848000-169860000	Weak transcription	HepG2	liver
18	chr1:169848400-169860600	Weak transcription	Fetal Heart	heart
19	chr1:169848800-169859000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:169850200-169858200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:169850600-169858200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:169850800-169858200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:169851600-169858200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:169851600-169859800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:169851600-169861200	Weak transcription	Aorta	Aorta
26	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:169851800-169860000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:169852000-169860000	Weak transcription	Lung	lung
29	chr1:169852200-169858200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:169852600-169859000	Weak transcription	Esophagus	oesophagus
31	chr1:169852600-169859000	Weak transcription	Ovary	ovary
32	chr1:169852600-169859200	Weak transcription	Thymus	Thymus
33	chr1:169852600-169859800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:169852600-169860000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:169852600-169860000	Weak transcription	Colonic Mucosa	Colon
36	chr1:169852600-169860000	Weak transcription	Gastric	stomach
37	chr1:169852600-169861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:169852600-169861400	Weak transcription	Brain Germinal Matrix	brain
39	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:169852800-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:169853600-169858800	Strong transcription	Primary B cells from cord blood	blood
42	chr1:169853800-169858200	Strong transcription	Fetal Thymus	thymus
43	chr1:169853800-169859600	Weak transcription	Fetal Intestine Small	intestine
44	chr1:169853800-169861400	Weak transcription	Fetal Stomach	stomach
45	chr1:169854000-169858200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:169854000-169858200	Strong transcription	Placenta	Placenta
47	chr1:169854400-169858200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:169854600-169858600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:169855000-169858200	Strong transcription	NHEK	skin
50	chr1:169855000-169861400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links