Variant report

Variant	rs10478230
Chromosome Location	chr5:114713898-114713899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114713336..114714974-chr5:114920219..114921988,2	MCF-7	breast:
2	chr5:114711869..114714907-chr5:114878578..114880723,3	MCF-7	breast:
3	chr5:114713804..114715548-chr5:114724717..114726881,2	MCF-7	breast:
4	chr5:114712072..114714398-chr5:114878860..114881275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145780	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10036686	0.93[EUR][1000 genomes]
rs10052230	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10052335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10054091	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10068248	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10072589	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10077253	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10078844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10085045	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10477528	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10477529	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10478229	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10478231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109015	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1109016	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12332367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2004680	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2605185	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs269502	0.85[EUR][1000 genomes]
rs3752047	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3752048	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3752050	0.82[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3752051	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[ASN][1000 genomes]
rs3752052	0.82[CEU][hapmap];0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3885971	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs749760	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7713623	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7713947	0.82[CEU][hapmap];0.89[CHB][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9986244	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9986246	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription 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 target site	28 gene(s)	inside rSNPs	diseases
2	esv2757132	chr5:114697260-114737583	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	esv2759370	chr5:114697260-114737583	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv882731	chr5:114702503-114721081	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv882732	chr5:114702503-114722599	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv882733	chr5:114702503-114726351	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	esv3470654	chr5:114706116-114721234	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3470655	chr5:114706116-114721234	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv1025594	chr5:114706443-114721081	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv441963	chr5:114706443-114721085	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
11	esv34270	chr5:114709101-114721101	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
12	esv34634	chr5:114709137-114723044	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	esv34713	chr5:114709137-114723044	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10478230	PGGT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114700200-114715800	Weak transcription	Pancreas	Pancrea
2	chr5:114702000-114717800	Weak transcription	Right Atrium	heart
3	chr5:114708200-114720600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:114711400-114714600	Enhancers	Fetal Muscle Leg	muscle
5	chr5:114712800-114714000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:114712800-114714000	Enhancers	Fetal Intestine Large	intestine
7	chr5:114712800-114714200	Enhancers	NHEK	skin
8	chr5:114712800-114715400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr5:114712800-114717400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:114713000-114716200	Enhancers	GM12878-XiMat	blood
11	chr5:114713200-114714000	Enhancers	Stomach Mucosa	stomach
12	chr5:114713200-114716200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:114713200-114716400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:114713400-114714000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr5:114713400-114714800	Enhancers	Small Intestine	intestine
16	chr5:114713600-114714000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:114713600-114714000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:114713600-114714000	Enhancers	Left Ventricle	heart
19	chr5:114713600-114714000	Enhancers	HSMM	muscle
20	chr5:114713600-114714200	Enhancers	Fetal Intestine Small	intestine
21	chr5:114713600-114714600	Enhancers	Psoas Muscle	Psoas
22	chr5:114713600-114714600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:114713600-114714800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:114713600-114716200	Enhancers	Duodenum Mucosa	Duodenum
25	chr5:114713800-114714000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:114713800-114714000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:114713800-114714000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:114713800-114714000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:114713800-114714000	Enhancers	Stomach Smooth Muscle	stomach
30	chr5:114713800-114714000	Enhancers	HSMMtube	muscle
31	chr5:114713800-114714000	Enhancers	NH-A	brain
32	chr5:114713800-114714000	Enhancers	Osteobl	bone
33	chr5:114713800-114714200	Enhancers	Hela-S3	cervix
34	chr5:114713800-114714200	Enhancers	NHDF-Ad	bronchial
35	chr5:114713800-114714200	Enhancers	NHLF	lung
36	chr5:114713800-114714400	Weak transcription	Esophagus	oesophagus
37	chr5:114713800-114714800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:114713800-114714800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr5:114713800-114715000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:114713800-114715000	Weak transcription	Fetal Kidney	kidney
41	chr5:114713800-114715000	Weak transcription	HMEC	breast
42	chr5:114713800-114716200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr5:114713800-114717000	Weak transcription	HUVEC	blood vessel
44	chr5:114713800-114719400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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