Variant report

Variant	rs17036996
Chromosome Location	chr2:48071255-48071256
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48070745..48074263-chr2:48075364..48078166,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10495947	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17037002	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17037018	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17037038	0.92[CEU][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17037055	1.00[YRI][hapmap]
rs17037064	0.91[YRI][hapmap]
rs2134056	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60154625	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60866242	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6704872	0.89[ASW][hapmap];0.91[CEU][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6714441	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6723441	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73929251	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7572674	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7587289	0.89[ASW][hapmap];0.85[CEU][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv962066	chr2:48061837-48072383	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17036996	PREPL	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48031400-48072600	Weak transcription	Stomach Mucosa	stomach
2	chr2:48038200-48071400	Weak transcription	Fetal Heart	heart
3	chr2:48043400-48088600	Weak transcription	Pancreas	Pancrea
4	chr2:48045800-48071600	Weak transcription	Aorta	Aorta
5	chr2:48048200-48072400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:48048600-48080600	Weak transcription	NHLF	lung
7	chr2:48049200-48096000	Weak transcription	Gastric	stomach
8	chr2:48050200-48072400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:48051600-48073400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:48058200-48074000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:48060200-48093000	Weak transcription	Psoas Muscle	Psoas
12	chr2:48061400-48093800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:48061600-48076000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:48062600-48080800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr2:48063000-48076000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:48063600-48074400	Weak transcription	Colonic Mucosa	Colon
17	chr2:48063800-48081800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:48063800-48083600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:48064000-48095200	Weak transcription	Spleen	Spleen
20	chr2:48064200-48081800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:48064400-48084800	Weak transcription	NHEK	skin
22	chr2:48065000-48072400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:48065000-48074200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:48065000-48081000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:48065200-48072000	Weak transcription	Esophagus	oesophagus
26	chr2:48065200-48086600	Weak transcription	Fetal Brain Female	brain
27	chr2:48065400-48071800	Weak transcription	Lung	lung
28	chr2:48065400-48073200	Weak transcription	Fetal Intestine Small	intestine
29	chr2:48065400-48074000	Weak transcription	Fetal Stomach	stomach
30	chr2:48065400-48098200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:48065400-48114000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:48066000-48072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:48066000-48085200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:48066000-48097400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:48066000-48100400	Weak transcription	Thymus	Thymus
36	chr2:48066200-48072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr2:48066200-48080000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:48066200-48080800	Weak transcription	HSMMtube	muscle
39	chr2:48066200-48084000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:48066200-48085400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:48066200-48094600	Weak transcription	Fetal Kidney	kidney
42	chr2:48066400-48071800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:48066400-48072400	Weak transcription	Primary B cells from cord blood	blood
44	chr2:48066400-48073200	Weak transcription	Brain Germinal Matrix	brain
45	chr2:48066400-48074400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:48066400-48083200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr2:48066400-48085400	Weak transcription	Osteobl	bone
48	chr2:48066400-48088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:48066400-48092200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:48066400-48097600	Weak transcription	Stomach Smooth Muscle	stomach

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