Variant report

Variant	rs11583896
Chromosome Location	chr1:153768982-153768983
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153768238..153771425-chr1:153928946..153932544,3	K562	blood:
2	chr1:153754545..153757490-chr1:153768363..153770074,2	MCF-7	breast:
3	chr1:153766040..153768161-chr1:153768242..153770371,2	K562	blood:
4	chr1:153767682..153770597-chr1:153957509..153960455,2	K562	blood:
5	chr1:153767106..153771449-chr1:153928785..153931237,4	MCF-7	breast:
6	chr1:153768275..153771240-chr1:153939698..153941215,2	MCF-7	breast:
7	chr1:153747748..153750181-chr1:153767825..153770639,2	MCF-7	breast:
8	chr1:153767840..153772262-chr1:153949074..153953547,7	MCF-7	breast:
9	chr1:153768238..153769957-chr1:153929788..153932544,2	K562	blood:
10	chr1:153761470..153763413-chr1:153768542..153770993,2	MCF-7	breast:
11	chr1:153768289..153770739-chr1:153938649..153941586,3	MCF-7	breast:
12	chr1:153768185..153769953-chr1:153961473..153965638,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143578	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000143545	Chromatin interaction
ENSG00000160741	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000231827	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143543	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10127983	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs10559	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs10752613	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796956	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908557	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs10908558	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1110165	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs11264532	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs11264619	0.82[AFR][1000 genomes]
rs11264680	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11264743	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11581644	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11583152	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11585416	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11587151	0.80[ASN][1000 genomes]
rs11589857	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11590099	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs12022158	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12022730	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12027783	0.82[AFR][1000 genomes]
rs12028398	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12032914	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12033835	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs12038577	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12041920	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12042562	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12042989	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[ASN][1000 genomes]
rs12043350	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12401565	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12403956	0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[TSI][hapmap]
rs12564669	0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs12567313	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1572788	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs34805562	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3748848	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs3791187	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs4077168	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4363451	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4391701	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4508047	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4520447	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4595397	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4612664	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845357	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap]
rs4845576	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845578	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845583	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs58095661	0.82[AFR][1000 genomes]
rs59308681	0.80[ASN][1000 genomes]
rs59340135	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs59678326	0.80[ASN][1000 genomes]
rs6666703	0.82[AFR][1000 genomes]
rs6680140	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6694061	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6700451	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72694220	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72694231	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72694234	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7512766	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7537691	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7552274	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8450	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs946682	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9660089	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
9	nsv515962	chr1:153752139-153773429	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11583896	SCNM1	cis	cerebellum	SCAN
rs11583896	LASS2	cis	parietal	SCAN
rs11583896	SLC27A3	cis	cerebellum	SCAN
rs11583896	RAG1AP1	cis	cerebellum	SCAN
rs11583896	GATAD2B	cis	cerebellum	SCAN
rs11583896	SLC39A1	cis	cerebellum	SCAN
rs11583896	SPRR2D	cis	parietal	SCAN
rs11583896	RAB13	cis	lymphoblastoid	seeQTL
rs11583896	CRTC2	cis	lymphoblastoid	seeQTL
rs11583896	CRTC2	cis	multi-tissue	Pritchard
rs11583896	PKLR	cis	parietal	SCAN
rs11583896	HAX1	cis	parietal	SCAN
rs11583896	FLG	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153757000-153779200	Weak transcription	Dnd41	blood
2	chr1:153762400-153776600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:153762600-153777600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:153762600-153777600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:153762600-153779600	Weak transcription	Gastric	stomach
6	chr1:153762600-153779600	Weak transcription	Pancreas	Pancrea
7	chr1:153763400-153772000	Weak transcription	Lung	lung
8	chr1:153763600-153771600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:153763600-153772000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:153763600-153776800	Weak transcription	Right Atrium	heart
11	chr1:153763600-153777800	Weak transcription	Fetal Intestine Large	intestine
12	chr1:153763600-153780000	Weak transcription	Aorta	Aorta
13	chr1:153763600-153780000	Weak transcription	Ovary	ovary
14	chr1:153763600-153780800	Weak transcription	Colonic Mucosa	Colon
15	chr1:153763800-153773200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:153763800-153779400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:153764000-153777000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:153764000-153777800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:153764000-153779600	Weak transcription	Brain Angular Gyrus	brain
20	chr1:153764400-153769000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:153764400-153769600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:153764400-153772200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:153764400-153774000	Weak transcription	Osteobl	bone
24	chr1:153764400-153776000	Weak transcription	HSMMtube	muscle
25	chr1:153764400-153777600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:153764400-153777600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:153764400-153778200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:153764400-153779600	Weak transcription	Brain Anterior Caudate	brain
29	chr1:153764600-153769400	Weak transcription	Fetal Thymus	thymus
30	chr1:153764600-153776000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:153764600-153777600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:153764600-153777800	Weak transcription	NHLF	lung
33	chr1:153764800-153771800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:153764800-153772000	Weak transcription	Esophagus	oesophagus
35	chr1:153764800-153773400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:153764800-153776000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:153764800-153776200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:153765000-153775600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:153765200-153769600	Weak transcription	Primary B cells from cord blood	blood
40	chr1:153765200-153769600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr1:153765400-153775000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:153765400-153775000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr1:153765600-153769200	Weak transcription	GM12878-XiMat	blood
44	chr1:153765600-153769600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:153766400-153769600	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:153766600-153770600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:153767000-153769200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:153767000-153770400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr1:153767000-153779400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:153767200-153769000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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