Variant report

Variant	rs12565932
Chromosome Location	chr1:160967455-160967456
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

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	chr1:160965945..160967708-chr1:160990265..160992249,2	K562	blood:
4	chr1:160965921..160968886-chr1:161007500..161010236,2	K562	blood:
5	chr1:160965718..160969126-chr1:160976993..160979194,4	K562	blood:
6	chr1:160966862..160967727-chr1:160990146..160990789,3	K562	blood:
7	chr1:160967182..160967792-chr1:160989065..160989909,2	K562	blood:
8	chr1:160965718..160967539-chr1:160977694..160979398,2	K562	blood:
9	chr1:160967112..160967785-chr1:161067206..161068112,4	MCF-7	breast:
10	chr1:160967186..160969825-chr1:161127897..161129470,2	MCF-7	breast:
11	chr1:160966815..160967738-chr1:161109054..161109807,2	K562	blood:
12	chr1:160964763..160967593-chr1:161005630..161008574,2	MCF-7	breast:
13	chr1:160967150..160969611-chr1:160987527..160989808,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000158769	Chromatin interaction
ENSG00000224985	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000143258	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];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1062826	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]
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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265540	0.87[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	0.89[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	0.94[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	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[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];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12401336	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[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	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12408778	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17384360	0.94[CHB][hapmap]
rs17388108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1806774	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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];0.99[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];0.99[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];0.99[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];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251728	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255852	0.81[JPT][hapmap]
rs2297219	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297222	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.99[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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481083	0.92[AMR][1000 genomes];0.93[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];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2481085	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2483145	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774274	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2988726	0.95[AMR][1000 genomes];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41267951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269993	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4339888	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs55728374	0.83[AMR][1000 genomes]
rs61802231	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61803664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61803665	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[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	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812741	0.95[AMR][1000 genomes];0.99[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];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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
rs12565932	OR6N2	cis	parietal	SCAN
rs12565932	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs12565932	ROBLD3	cis	cerebellum	SCAN
rs12565932	ISG20L2	cis	cerebellum	SCAN
rs12565932	ARHGEF11	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160948600-160968000	Weak transcription	Ovary	ovary
2	chr1:160953800-160968200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:160957800-160968000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:160960000-160968000	Weak transcription	Pancreas	Pancrea
5	chr1:160960000-160970200	Weak transcription	Right Ventricle	heart
6	chr1:160960200-160967600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:160960200-160967600	Weak transcription	Fetal Muscle Leg	muscle
8	chr1:160960200-160968000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:160960200-160968400	Weak transcription	Left Ventricle	heart
10	chr1:160960400-160967600	Weak transcription	Fetal Stomach	stomach
11	chr1:160960400-160968000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:160960400-160968200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:160960400-160968200	Weak transcription	Fetal Brain Female	brain
14	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
15	chr1:160960600-160967600	Weak transcription	Primary T cells from cord blood	blood
16	chr1:160960600-160968000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:160960600-160968000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160960600-160968000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:160960600-160968000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:160960600-160968000	Weak transcription	Thymus	Thymus
21	chr1:160960600-160968400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:160960600-160968600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:160960600-160968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:160960600-160968800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:160960600-160968800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:160960600-160968800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:160960600-160969000	Weak transcription	Dnd41	blood
28	chr1:160960600-160969600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
30	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:160962600-160968000	Weak transcription	Spleen	Spleen
32	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
33	chr1:160964400-160967800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr1:160964400-160968800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:160964400-160972600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:160964600-160967600	Genic enhancers	NHEK	skin
37	chr1:160965000-160967600	Enhancers	A549	lung
38	chr1:160965000-160967800	Enhancers	Hela-S3	cervix
39	chr1:160965000-160971800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr1:160965200-160968400	Weak transcription	Colonic Mucosa	Colon
41	chr1:160965400-160969400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:160965400-160972600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:160965800-160969800	Weak transcription	HSMM	muscle
44	chr1:160966200-160970600	Strong transcription	Fetal Intestine Large	intestine
45	chr1:160966400-160971000	Weak transcription	Psoas Muscle	Psoas
46	chr1:160966600-160967600	Strong transcription	Liver	Liver
47	chr1:160966600-160967800	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr1:160966600-160968200	Weak transcription	Small Intestine	intestine
49	chr1:160966600-160968400	Weak transcription	Brain Germinal Matrix	brain
50	chr1:160966600-160971800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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