Variant report

Variant	rs2481084
Chromosome Location	chr1:160989614-160989615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160989106..160992104-chr1:161101728..161103686,4	K562	blood:
2	chr1:160970990..160972886-chr1:160988444..160990539,2	MCF-7	breast:
3	chr1:160957625..160960589-chr1:160987961..160989680,2	K562	blood:
4	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
5	chr1:160989498..160991645-chr1:161056781..161059472,2	MCF-7	breast:
6	chr1:160988253..160990584-chr1:161134900..161137234,2	K562	blood:
7	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
8	chr1:160967150..160969611-chr1:160987527..160989808,2	K562	blood:
9	chr1:160989097..160992016-chr1:161278410..161280382,2	K562	blood:
10	chr1:160987801..160992609-chr1:161065993..161069595,4	MCF-7	breast:
11	chr1:160986835..160990359-chr1:161086146..161091164,5	K562	blood:
12	chr1:160967182..160967792-chr1:160989065..160989909,2	K562	blood:
13	chr1:160969730..160971940-chr1:160985751..160989711,3	MCF-7	breast:
14	chr1:160988368..160992141-chr1:161085559..161090183,5	MCF-7	breast:
15	chr1:160638640..160640892-chr1:160989316..160991533,2	K562	blood:
16	chr1:160988517..160990791-chr1:161000780..161003550,2	K562	blood:
17	chr1:160988859..160991431-chr1:161086289..161089011,2	K562	blood:
18	chr1:160986477..160990791-chr1:161000780..161004789,4	K562	blood:
19	chr1:160987861..160992104-chr1:161101436..161104060,5	K562	blood:
20	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:
21	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
22	chr1:160988315..160990144-chr1:161088244..161090577,2	MCF-7	breast:
23	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
24	chr1:160989601..160993379-chr1:161101301..161104263,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000158796	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000143224	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000235101	Chromatin interaction
ENSG00000158887	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000232879	Chromatin interaction
ENSG00000228863	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1044478	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1062826	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]
rs1062827	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];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11265540	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11265542	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799478	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11799521	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11801586	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11801591	0.90[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs11802727	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs11805856	0.83[AMR][1000 genomes]
rs11807930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12401336	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12403334	0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs12405782	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12408778	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565932	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];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17384360	0.94[CHB][hapmap]
rs17388108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1806774	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2073655	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073656	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2073658	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2243427	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247459	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247596	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2247790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2251597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255852	0.81[JPT][hapmap]
rs2265243	0.82[ASN][1000 genomes]
rs2297219	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2297221	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];0.99[ASN][1000 genomes]
rs2297222	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2481080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481081	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2483145	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2774274	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2988726	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3119321	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737785	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3737787	0.87[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41267947	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41267949	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41267951	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41269993	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4339888	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55728374	0.85[EUR][1000 genomes]
rs61802231	0.81[AMR][1000 genomes]
rs61803664	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61803665	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61803671	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61803672	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72712854	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs812741	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs836	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];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs869985	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];0.99[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
rs2481084	PEAR1	cis	parietal	SCAN
rs2481084	ISG20L2	cis	cerebellum	SCAN
rs2481084	OR10J5	cis	cerebellum	SCAN
rs2481084	ARHGEF11	cis	cerebellum	SCAN
rs2481084	ROBLD3	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160984200-160989800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr1:160984400-160989800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr1:160984400-160989800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:160984400-160989800	Weak transcription	Right Ventricle	heart
5	chr1:160984400-160990800	Weak transcription	HSMMtube	muscle
6	chr1:160984400-160991000	Weak transcription	HSMM	muscle
7	chr1:160986400-160989800	Enhancers	Pancreas	Pancrea
8	chr1:160987600-160990200	Enhancers	Spleen	Spleen
9	chr1:160987800-160989800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:160987800-160989800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:160987800-160989800	Enhancers	Fetal Thymus	thymus
12	chr1:160987800-160990400	Weak transcription	Aorta	Aorta
13	chr1:160987800-160990600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:160987800-160990800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr1:160988000-160989800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:160988000-160989800	Weak transcription	Left Ventricle	heart
17	chr1:160988000-160992000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:160988200-160989800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:160988200-160989800	Weak transcription	Small Intestine	intestine
20	chr1:160988400-160991800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:160988400-160991800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:160988400-160991800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:160988600-160989800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:160988600-160989800	Enhancers	Primary B cells from peripheral blood	blood
25	chr1:160988600-160989800	Weak transcription	Lung	lung
26	chr1:160988600-160990000	Active TSS	Rectal Smooth Muscle	rectum
27	chr1:160988600-160990600	Flanking Active TSS	HUVEC	blood vessel
28	chr1:160988600-160990800	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr1:160988600-160990800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr1:160988600-160991200	Active TSS	Esophagus	oesophagus
31	chr1:160988600-160992000	Active TSS	H1 Cell Line	embryonic stem cell
32	chr1:160988600-160992200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:160988800-160989800	Weak transcription	Gastric	stomach
34	chr1:160988800-160989800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:160988800-160991000	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:160988800-160991800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:160988800-160991800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr1:160988800-160991800	Active TSS	Colonic Mucosa	Colon
39	chr1:160988800-160992000	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr1:160989000-160989800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:160989000-160989800	Flanking Active TSS	HepG2	liver
42	chr1:160989000-160989800	Flanking Active TSS	HMEC	breast
43	chr1:160989000-160991400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:160989000-160991400	Active TSS	NHEK	skin
45	chr1:160989000-160991600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:160989000-160991800	Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr1:160989000-160992000	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:160989000-160992000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:160989200-160990600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr1:160989200-160991800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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