Variant report

Variant	rs10935323
Chromosome Location	chr3:139110135-139110136
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr3:139110050-139110328	K562	blood:	n/a	n/a
2	POLR2A	chr3:139106214-139110153	IMR90	lung:	n/a	n/a
3	POLR2A	chr3:139109825-139110506	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:139107677-139110513	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:139109720..139111742-chr3:139198602..139200666,2	K562	blood:
2	chr3:139061660..139066893-chr3:139105523..139110764,11	K562	blood:
3	chr3:139063205..139066777-chr3:139105523..139110764,7	K562	blood:

Variant related genes	Relation type
COPB2	TF binding region
ENSG00000175110	Chromatin interaction
ENSG00000114113	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1044826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10460845	0.89[ASN][1000 genomes]
rs1080371	0.83[CHD][hapmap]
rs10935320	0.97[ASN][1000 genomes]
rs12488939	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494556	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12494806	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12695698	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695699	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12695700	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060697	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13071857	0.82[EUR][1000 genomes]
rs13074208	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13083195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085888	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13086868	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13089007	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089052	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13089090	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13092507	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13092935	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586861	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1586863	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1586864	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs167187	0.83[CHD][hapmap]
rs17336869	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs188421	0.83[CHD][hapmap]
rs1907687	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2165139	0.84[ASN][1000 genomes]
rs2233811	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2233815	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2349059	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34623690	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772877	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772878	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3772879	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3821544	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821545	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4544576	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4683464	0.83[CHD][hapmap]
rs4683818	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6439860	0.83[CHD][hapmap]
rs6771831	0.83[CHD][hapmap]
rs67929453	0.98[ASN][1000 genomes]
rs7374385	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs747346	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9289576	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs964227	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs973691	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9812192	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9818691	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]
rs9825064	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9831108	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834607	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9835241	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848241	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9849039	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9849578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853350	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859864	0.83[CHD][hapmap]
rs9860201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860521	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9868544	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9882014	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10935323	BPESC1	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139106600-139110400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr3:139107000-139110200	Active TSS	A549	lung
3	chr3:139107200-139110200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:139109200-139110200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:139109200-139110200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr3:139109200-139123400	Weak transcription	Lung	lung
7	chr3:139109400-139110600	Enhancers	Fetal Heart	heart
8	chr3:139109400-139110600	Enhancers	Fetal Lung	lung
9	chr3:139109400-139110800	Enhancers	Left Ventricle	heart
10	chr3:139109400-139123400	Weak transcription	Aorta	Aorta
11	chr3:139109600-139110200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:139109600-139110200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr3:139109600-139110400	Enhancers	Fetal Kidney	kidney
14	chr3:139109600-139110400	Flanking Active TSS	HepG2	liver
15	chr3:139109600-139110600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:139109600-139110600	Enhancers	Liver	Liver
17	chr3:139109600-139110600	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:139109600-139111000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:139109600-139111000	Enhancers	Fetal Intestine Large	intestine
20	chr3:139109600-139112800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:139109600-139118000	Weak transcription	Brain Angular Gyrus	brain
22	chr3:139109600-139123400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:139109800-139110200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:139109800-139110200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:139109800-139110200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:139109800-139110200	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:139109800-139110200	Enhancers	Fetal Intestine Small	intestine
28	chr3:139109800-139110200	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr3:139109800-139110200	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr3:139109800-139110400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:139109800-139110400	Enhancers	GM12878-XiMat	blood
32	chr3:139109800-139110400	Enhancers	NHDF-Ad	bronchial
33	chr3:139109800-139110600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:139109800-139110600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:139109800-139110600	Enhancers	Colon Smooth Muscle	Colon
36	chr3:139109800-139110600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:139109800-139112800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:139109800-139117200	Weak transcription	Psoas Muscle	Psoas
39	chr3:139109800-139119800	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:139110000-139110200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:139110000-139110200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:139110000-139110200	Enhancers	Brain Substantia Nigra	brain
43	chr3:139110000-139110200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:139110000-139110200	Enhancers	Stomach Mucosa	stomach
45	chr3:139110000-139110400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:139110000-139110400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:139110000-139110600	Flanking Active TSS	K562	blood
48	chr3:139110000-139117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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