Variant report

Variant	rs1062826
Chromosome Location	chr1:160968005-160968006
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160965718..160968387-chr1:160991950..160993671,3	MCF-7	breast:
2	chr1:160967045..160969239-chr1:160970582..160972680,3	K562	blood:
3	chr1:160965921..160968886-chr1:161007500..161010236,2	K562	blood:
4	chr1:160965718..160969126-chr1:160976993..160979194,4	K562	blood:
5	chr1:160967186..160969825-chr1:161127897..161129470,2	MCF-7	breast:
6	chr1:160967150..160969611-chr1:160987527..160989808,2	K562	blood:

Variant related genes	Relation type
ENSG00000270149	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000224985	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1044478	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265540	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265542	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11799478	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11799521	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11801586	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11801591	0.90[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11802727	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs11805856	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11807930	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12401336	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12403334	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs12405782	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12408778	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565932	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384360	0.94[CHB][hapmap]
rs17388108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1806774	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073655	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs2073656	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes]
rs2073658	0.89[AMR][1000 genomes]
rs2243427	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247459	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2247790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251597	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251728	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255852	0.81[JPT][hapmap]
rs2297219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297222	0.91[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2481080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481081	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481083	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481084	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481085	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2483145	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774274	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2988726	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3119321	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737785	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737787	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs41267947	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269993	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339888	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55728374	0.83[AMR][1000 genomes]
rs61802231	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61803664	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61803665	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61803671	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61803672	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72712854	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812741	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1062826	ROBLD3	cis	cerebellum	SCAN
rs1062826	ISG20L2	cis	cerebellum	SCAN
rs1062826	PEAR1	cis	parietal	SCAN
rs1062826	OR10J5	cis	cerebellum	SCAN
rs1062826	ARHGEF11	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160953800-160968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:160960000-160970200	Weak transcription	Right Ventricle	heart
3	chr1:160960200-160968400	Weak transcription	Left Ventricle	heart
4	chr1:160960400-160968200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160960400-160968200	Weak transcription	Fetal Brain Female	brain
6	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
7	chr1:160960600-160968400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:160960600-160968600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:160960600-160968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:160960600-160968800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:160960600-160968800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:160960600-160968800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:160960600-160969000	Weak transcription	Dnd41	blood
14	chr1:160960600-160969600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
16	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
18	chr1:160964400-160968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:160964400-160972600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:160965000-160971800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr1:160965200-160968400	Weak transcription	Colonic Mucosa	Colon
22	chr1:160965400-160969400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:160965400-160972600	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:160965800-160969800	Weak transcription	HSMM	muscle
25	chr1:160966200-160970600	Strong transcription	Fetal Intestine Large	intestine
26	chr1:160966400-160971000	Weak transcription	Psoas Muscle	Psoas
27	chr1:160966600-160968200	Weak transcription	Small Intestine	intestine
28	chr1:160966600-160968400	Weak transcription	Brain Germinal Matrix	brain
29	chr1:160966600-160971800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:160966600-160971800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:160966800-160968200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:160966800-160968200	Genic enhancers	Duodenum Mucosa	Duodenum
33	chr1:160966800-160968600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:160966800-160971200	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:160966800-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:160967000-160968200	Enhancers	Stomach Mucosa	stomach
37	chr1:160967000-160968200	Genic enhancers	K562	blood
38	chr1:160967000-160968400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:160967000-160969600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:160967000-160971200	Strong transcription	Fetal Thymus	thymus
41	chr1:160967000-160971600	Strong transcription	Esophagus	oesophagus
42	chr1:160967000-160971800	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:160967000-160971800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:160967000-160972400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:160967400-160968200	Genic enhancers	Fetal Intestine Small	intestine
46	chr1:160967400-160969600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:160967400-160970000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:160967400-160971200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:160967400-160972400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:160967600-160968200	Weak transcription	Primary B cells from peripheral blood	blood

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