Variant report

Variant	rs1341053
Chromosome Location	chr10:112624417-112624418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:112619976..112621835-chr10:112622055..112625024,2	MCF-7	breast:
2	chr10:112589697..112592145-chr10:112622610..112625288,3	MCF-7	breast:
3	chr10:112610748..112613703-chr10:112623981..112626805,2	MCF-7	breast:
4	chr10:112532259..112533809-chr10:112624072..112626990,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10787287	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs10787289	0.89[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10787292	0.88[TSI][hapmap]
rs1322995	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1341051	1.00[ASW][hapmap];0.94[CEU][hapmap];0.80[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1410057	0.88[TSI][hapmap]
rs4918607	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7067540	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7086350	0.82[TSI][hapmap]
rs7095404	0.88[TSI][hapmap]
rs7895872	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7899762	0.87[EUR][1000 genomes]

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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1341053	XPNPEP1	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112611200-112630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:112617000-112624600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr10:112617000-112624600	Enhancers	Primary B cells from peripheral blood	blood
4	chr10:112617000-112624600	Enhancers	Primary T cells fromperipheralblood	blood
5	chr10:112617000-112624600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr10:112617000-112628600	Enhancers	Placenta	Placenta
7	chr10:112617800-112630600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:112618000-112624600	Weak transcription	Left Ventricle	heart
9	chr10:112618400-112630800	Enhancers	Fetal Thymus	thymus
10	chr10:112618600-112624600	Enhancers	Duodenum Mucosa	Duodenum
11	chr10:112619400-112624800	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr10:112619800-112627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:112620000-112624600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr10:112620000-112624600	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:112620000-112624800	Weak transcription	Psoas Muscle	Psoas
16	chr10:112620200-112624600	Enhancers	NHEK	skin
17	chr10:112620400-112624600	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:112620600-112624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:112621000-112624600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr10:112621000-112624600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr10:112621000-112625200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:112621000-112630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr10:112621000-112631000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:112621200-112624600	Weak transcription	Colonic Mucosa	Colon
25	chr10:112621200-112624600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr10:112621200-112624600	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr10:112621200-112630400	Weak transcription	Gastric	stomach
28	chr10:112621200-112630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:112621200-112630600	Weak transcription	Brain Substantia Nigra	brain
30	chr10:112621800-112624600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr10:112621800-112624600	Enhancers	NHDF-Ad	bronchial
32	chr10:112621800-112628600	Enhancers	Fetal Muscle Leg	muscle
33	chr10:112622000-112626200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr10:112622000-112628400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:112622200-112624600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr10:112622200-112624600	Enhancers	HSMMtube	muscle
37	chr10:112622200-112626400	Enhancers	Fetal Stomach	stomach
38	chr10:112622200-112628400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr10:112622400-112624600	Weak transcription	Pancreas	Pancrea
40	chr10:112623000-112630600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr10:112623200-112628200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr10:112623400-112624600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr10:112623400-112624600	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr10:112623400-112627600	Enhancers	Fetal Intestine Small	intestine
45	chr10:112623400-112631000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr10:112623600-112624600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr10:112623600-112627400	Enhancers	Fetal Muscle Trunk	muscle
48	chr10:112623800-112624600	Enhancers	Rectal Smooth Muscle	rectum
49	chr10:112623800-112624600	Enhancers	Hela-S3	cervix
50	chr10:112623800-112624800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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