Variant report

Variant	rs2864794
Chromosome Location	chr3:145866370-145866371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:145783058..145783996-chr3:145865459..145867166,7	MCF-7	breast:
2	chr3:145783014..145783624-chr3:145865958..145866776,2	MCF-7	breast:
3	chr3:145862765..145866552-chr3:145878072..145880810,4	MCF-7	breast:
4	chr3:145865509..145867074-chr3:145870719..145872599,2	K562	blood:

Variant related genes	Relation type
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10513277	0.83[CHB][hapmap]
rs12632001	0.84[CHD][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap]
rs1449442	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1913185	0.83[CHB][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap]
rs3749282	0.87[ASW][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs3792347	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs58874363	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59384952	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59850864	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67154251	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67325724	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67671074	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6787634	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv877613	chr3:145833232-145912055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1011146	chr3:145859022-145911429	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv1012485	chr3:145861750-145947125	Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv536758	chr3:145861750-145947125	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2864794	PAX6	trans	cerebellum	SCAN
rs2864794	PLSCR4	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145832000-145870800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:145835800-145874000	Weak transcription	Psoas Muscle	Psoas
3	chr3:145840400-145874000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:145856400-145875800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:145858800-145866400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr3:145860400-145875600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:145860600-145868800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:145860800-145870000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:145860800-145873800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:145860800-145874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:145860800-145874000	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:145861000-145869000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:145861000-145870200	Weak transcription	Brain Anterior Caudate	brain
14	chr3:145861000-145876400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:145861400-145866400	Weak transcription	NHDF-Ad	bronchial
16	chr3:145861400-145870200	Weak transcription	Small Intestine	intestine
17	chr3:145861400-145870600	Weak transcription	NH-A	brain
18	chr3:145861600-145869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:145861600-145870000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:145861800-145866600	Weak transcription	Aorta	Aorta
21	chr3:145861800-145866800	Weak transcription	Fetal Kidney	kidney
22	chr3:145861800-145867600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:145861800-145870200	Weak transcription	Brain Substantia Nigra	brain
24	chr3:145861800-145870400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:145861800-145870800	Weak transcription	Pancreas	Pancrea
26	chr3:145861800-145872200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:145861800-145873800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:145861800-145873800	Weak transcription	HSMMtube	muscle
29	chr3:145861800-145874000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:145861800-145874000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:145862000-145871600	Strong transcription	HSMM	muscle
32	chr3:145862000-145873800	Weak transcription	NHLF	lung
33	chr3:145862400-145866400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:145862400-145874000	Weak transcription	Lung	lung
35	chr3:145862600-145870800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:145863600-145869000	Weak transcription	Fetal Stomach	stomach
37	chr3:145864000-145866800	Enhancers	Colon Smooth Muscle	Colon
38	chr3:145864200-145866800	Enhancers	Ovary	ovary
39	chr3:145864200-145867200	Enhancers	Liver	Liver
40	chr3:145864400-145869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:145864400-145870800	Weak transcription	Esophagus	oesophagus
42	chr3:145864400-145870800	Weak transcription	Gastric	stomach
43	chr3:145864400-145872200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:145864400-145873000	Genic enhancers	Osteobl	bone
45	chr3:145864600-145870000	Weak transcription	Right Ventricle	heart
46	chr3:145864600-145870800	Weak transcription	Right Atrium	heart
47	chr3:145864800-145870400	Weak transcription	HMEC	breast
48	chr3:145865000-145866400	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:145865200-145869000	Enhancers	Rectal Smooth Muscle	rectum
50	chr3:145865600-145867000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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