Variant report

Variant	rs10495947
Chromosome Location	chr2:48084562-48084563
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48079577..48082466-chr2:48083216..48086819,3	K562	blood:
2	chr2:48079893..48082466-chr2:48082894..48085745,2	K562	blood:
3	chr2:48084089..48084724-chr2:48333394..48334291,2	MCF-7	breast:
4	chr2:48082764..48087020-chr2:48130453..48135534,7	MCF-7	breast:
5	chr2:48083338..48085920-chr2:48132296..48135049,2	K562	blood:
6	chr2:48084015..48085613-chr2:48093041..48095480,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138081	Chromatin interaction
ENSG00000233230	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs17036996	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17037002	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17037018	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17037038	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17037055	1.00[YRI][hapmap]
rs17037064	0.91[YRI][hapmap]
rs2134056	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60154625	0.92[EUR][1000 genomes]
rs60866242	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6704872	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6714441	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6723441	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73929251	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7572674	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7587289	0.89[ASW][hapmap];0.93[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv930955	chr2:48040218-48121218	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv523013	chr2:48073117-48146122	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv874000	chr2:48078838-48291582	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10495947	PREPL	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48043400-48088600	Weak transcription	Pancreas	Pancrea
2	chr2:48049200-48096000	Weak transcription	Gastric	stomach
3	chr2:48060200-48093000	Weak transcription	Psoas Muscle	Psoas
4	chr2:48061400-48093800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:48064000-48095200	Weak transcription	Spleen	Spleen
6	chr2:48064400-48084800	Weak transcription	NHEK	skin
7	chr2:48065200-48086600	Weak transcription	Fetal Brain Female	brain
8	chr2:48065400-48098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:48065400-48114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:48066000-48085200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:48066000-48097400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:48066000-48100400	Weak transcription	Thymus	Thymus
13	chr2:48066200-48085400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:48066200-48094600	Weak transcription	Fetal Kidney	kidney
15	chr2:48066400-48085400	Weak transcription	Osteobl	bone
16	chr2:48066400-48088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:48066400-48092200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:48066400-48097600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:48066800-48088400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:48066800-48094200	Weak transcription	HSMM	muscle
21	chr2:48066800-48094400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:48067000-48084600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:48067000-48091800	Weak transcription	HUVEC	blood vessel
24	chr2:48067000-48094200	Weak transcription	HMEC	breast
25	chr2:48067000-48094800	Weak transcription	K562	blood
26	chr2:48067000-48095800	Weak transcription	Fetal Thymus	thymus
27	chr2:48067000-48122000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:48067600-48097600	Weak transcription	Dnd41	blood
29	chr2:48067800-48094400	Weak transcription	Right Atrium	heart
30	chr2:48070200-48084800	Weak transcription	Small Intestine	intestine
31	chr2:48070400-48091800	Weak transcription	Brain Substantia Nigra	brain
32	chr2:48072200-48093000	Weak transcription	Lung	lung
33	chr2:48073000-48095200	Weak transcription	Right Ventricle	heart
34	chr2:48073000-48096000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:48073600-48100000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr2:48074200-48085200	Weak transcription	Ovary	ovary
37	chr2:48075600-48085200	Weak transcription	Fetal Stomach	stomach
38	chr2:48075600-48094400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:48075800-48095800	Weak transcription	Fetal Intestine Large	intestine
40	chr2:48077000-48088600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:48077400-48094000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:48077600-48084600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:48077800-48089800	Weak transcription	GM12878-XiMat	blood
44	chr2:48078000-48090800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:48080000-48084800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:48080200-48088600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:48080400-48084800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:48081200-48084800	Weak transcription	A549	lung
49	chr2:48081200-48094200	Weak transcription	Fetal Lung	lung
50	chr2:48081400-48084800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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