Variant report

Variant	rs923001
Chromosome Location	chr3:136378415-136378416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136364480..136366014-chr3:136376930..136379520,2	MCF-7	breast:
2	chr3:136377566..136379306-chr3:136381547..136383907,2	K562	blood:
3	chr3:136371791..136373767-chr3:136377876..136379959,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10513016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];1.00[ASN][1000 genomes]
rs16843991	1.00[CHB][hapmap]
rs16844056	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[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];1.00[ASN][1000 genomes]
rs17466223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35644083	1.00[CHB][hapmap]
rs3931416	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4336059	1.00[CHB][hapmap]
rs55763637	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218376	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56308712	0.81[EUR][1000 genomes]
rs56888009	0.96[EUR][1000 genomes]
rs57466072	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681357	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58636237	0.85[EUR][1000 genomes]
rs59361983	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59616231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59696368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60014495	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs60270684	0.82[AFR][1000 genomes]
rs6439642	1.00[CHB][hapmap]
rs66470158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66471262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66637228	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66739346	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66902780	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66973954	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67231188	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67281610	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67303976	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67305360	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67546863	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs67621498	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6765239	1.00[CHB][hapmap]
rs67663578	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6773495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs67794070	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67888773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67902591	0.85[EUR][1000 genomes]
rs67923745	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6800969	1.00[CHB][hapmap]
rs68018658	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72975363	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73226130	0.81[EUR][1000 genomes]
rs73228025	0.91[EUR][1000 genomes]
rs73228037	0.94[EUR][1000 genomes]
rs73228040	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230052	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73230077	0.85[EUR][1000 genomes]
rs73230078	0.85[EUR][1000 genomes]
rs73230095	0.83[EUR][1000 genomes]
rs73231917	0.81[EUR][1000 genomes]
rs7623824	1.00[CHB][hapmap]
rs7636806	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7644471	1.00[CHB][hapmap]
rs7646563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820513	1.00[CHB][hapmap]
rs9869957	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1008866	chr3:136364511-136427790	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv877529	chr3:136364511-136487559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs923001	STAG1	cis	cerebellum	SCAN
rs923001	VCAN	trans	cerebellum	SCAN
rs923001	TMEM22	cis	cerebellum	SCAN
rs923001	IL20RB	cis	Nerve Tibial	GTEx
rs923001	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136357800-136387400	Weak transcription	Fetal Thymus	thymus
2	chr3:136365000-136396400	Weak transcription	Gastric	stomach
3	chr3:136365200-136381400	Weak transcription	Pancreas	Pancrea
4	chr3:136368200-136385000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:136369000-136386800	Weak transcription	Lung	lung
6	chr3:136370600-136385400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:136370800-136382800	Weak transcription	Ovary	ovary
8	chr3:136372000-136383200	Weak transcription	Aorta	Aorta
9	chr3:136373800-136382600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:136374400-136382600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:136374400-136387400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:136374400-136390000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:136374600-136381200	Weak transcription	Fetal Stomach	stomach
14	chr3:136374600-136384200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:136374600-136387400	Weak transcription	Primary T cells from cord blood	blood
16	chr3:136374600-136389400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:136374800-136383400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:136374800-136390000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:136375600-136390400	Weak transcription	Dnd41	blood
20	chr3:136376400-136387400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:136376600-136392200	Weak transcription	Placenta	Placenta
22	chr3:136376800-136381200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:136376800-136390400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:136377000-136386800	Weak transcription	Left Ventricle	heart
25	chr3:136377000-136387600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:136377000-136389400	Weak transcription	NHEK	skin
27	chr3:136377000-136390400	Weak transcription	Right Ventricle	heart
28	chr3:136377600-136378600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:136377600-136378600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:136377600-136378600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr3:136377600-136378600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:136377600-136378600	Enhancers	Adipose Nuclei	Adipose
33	chr3:136377600-136378800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:136377600-136379600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:136377800-136378600	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:136377800-136378600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr3:136377800-136378600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr3:136377800-136378600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:136377800-136378600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:136377800-136378600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:136377800-136378600	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr3:136377800-136378600	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr3:136377800-136378600	Active TSS	Brain Germinal Matrix	brain
44	chr3:136377800-136378600	Enhancers	Fetal Brain Male	brain
45	chr3:136377800-136378600	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:136377800-136378600	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:136377800-136378600	Enhancers	HSMMtube	muscle
48	chr3:136377800-136378600	Enhancers	NH-A	brain
49	chr3:136377800-136378600	Enhancers	NHLF	lung
50	chr3:136377800-136378800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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