Variant report

Variant	rs4142965
Chromosome Location	chr13:92013413-92013414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:92010635..92015807-chr13:92018550..92023163,4	MCF-7	breast:
2	chr13:92012792..92014958-chr13:92182258..92184358,2	K562	blood:
3	chr13:91794532..91796912-chr13:92012820..92014472,2	K562	blood:
4	chr13:92010540..92013547-chr13:92187635..92190322,4	K562	blood:
5	chr13:92009670..92013881-chr13:92375334..92379387,4	K562	blood:
6	chr13:90803949..90805680-chr13:92011552..92014384,2	K562	blood:
7	chr13:92010191..92014540-chr13:92229897..92231842,4	K562	blood:
8	chr13:92013384..92016331-chr13:92208566..92210959,3	K562	blood:
9	chr13:92010990..92013754-chr13:92321109..92322793,2	K562	blood:
10	chr13:92013396..92015675-chr13:92176730..92178777,2	K562	blood:
11	chr13:92011668..92014264-chr13:92248791..92250619,2	K562	blood:
12	chr13:92010929..92013926-chr13:92211896..92214067,2	K562	blood:
13	chr13:91889138..91891419-chr13:92011620..92013937,2	K562	blood:
14	chr13:92011581..92014280-chr13:92377653..92379925,3	K562	blood:
15	chr13:92013319..92015421-chr9:134129597..134132171,2	K562	blood:
16	chr13:92009508..92013495-chr13:92125822..92129742,3	K562	blood:
17	chr13:91999461..92007353-chr13:92008154..92015149,15	MCF-7	breast:
18	chr13:92011474..92015304-chr13:92379938..92384751,4	K562	blood:
19	chr13:92007380..92009324-chr13:92011441..92013491,2	MCF-7	breast:
20	chr13:92013065..92015045-chr13:92455620..92457213,2	K562	blood:
21	chr13:92010904..92013459-chr13:92248662..92250979,3	K562	blood:
22	chr13:92009784..92014607-chr13:92111183..92117003,5	K562	blood:
23	chr13:92012175..92013793-chr4:83348518..83351402,2	K562	blood:
24	chr13:92012440..92014538-chr13:92281006..92283955,2	K562	blood:
25	chr13:91919441..91922315-chr13:92012969..92015337,3	K562	blood:
26	chr13:91797508..91800057-chr13:92012976..92014999,2	K562	blood:
27	chr13:92010706..92013622-chr13:93006752..93008493,2	K562	blood:
28	chr13:91785529..91788379-chr13:92011883..92013618,2	K562	blood:
29	chr13:92011474..92014177-chr13:92380431..92383913,3	K562	blood:
30	chr13:92007619..92013984-chr13:92329606..92334220,7	K562	blood:
31	chr13:91920179..91922847-chr13:92012969..92015159,3	K562	blood:
32	chr13:92012879..92016310-chr13:92160976..92164923,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215417	Chromatin interaction
ENSG00000179399	Chromatin interaction
ENSG00000152795	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1330062	0.95[ASN][1000 genomes]
rs1330063	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1428	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4284505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4773624	0.99[ASN][1000 genomes]
rs4773625	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7319045	0.99[ASN][1000 genomes]
rs7319759	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7320878	0.96[CEU][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7322734	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7324173	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7336610	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs769040	0.88[YRI][hapmap]
rs8001004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002779	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9515919	0.99[ASN][1000 genomes]
rs9523304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9523307	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9523310	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9523312	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9523313	0.99[ASN][1000 genomes]
rs976547	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042947	chr13:91571040-92416897	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
2	nsv541871	chr13:91571040-92416897	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1946 gene(s)	inside rSNPs	diseases
3	esv1803618	chr13:91669587-92277699	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1945 gene(s)	inside rSNPs	diseases
4	nsv1050259	chr13:91759549-92152078	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
5	nsv541872	chr13:91759549-92152078	Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1944 gene(s)	inside rSNPs	diseases
6	nsv832679	chr13:91859467-92030220	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1943 gene(s)	inside rSNPs	diseases
7	esv1802171	chr13:91999737-92015977	Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1940 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4142965	GPC5	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001800-92015600	Weak transcription	Ovary	ovary
2	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
3	chr13:92003400-92014000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:92003600-92016600	Weak transcription	Gastric	stomach
5	chr13:92003600-92021200	Weak transcription	Right Ventricle	heart
6	chr13:92003600-92033200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr13:92004600-92021200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:92007800-92015200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr13:92008400-92014600	Weak transcription	Hela-S3	cervix
10	chr13:92008600-92014000	Weak transcription	Fetal Intestine Large	intestine
11	chr13:92008800-92013800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:92008800-92021000	Weak transcription	Osteobl	bone
13	chr13:92008800-92021400	Weak transcription	NHLF	lung
14	chr13:92009200-92016200	Enhancers	Liver	Liver
15	chr13:92009400-92014000	Weak transcription	Fetal Lung	lung
16	chr13:92009400-92014000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:92009400-92020000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr13:92009400-92020800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:92009600-92021200	Weak transcription	HSMMtube	muscle
20	chr13:92009600-92022200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:92009800-92014800	Weak transcription	Left Ventricle	heart
22	chr13:92009800-92021200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr13:92009800-92021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:92010000-92013800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr13:92010000-92014400	Weak transcription	Brain Germinal Matrix	brain
26	chr13:92010000-92014800	Enhancers	HepG2	liver
27	chr13:92010000-92021000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:92010000-92021000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:92010200-92021200	Weak transcription	NH-A	brain
30	chr13:92010200-92021600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr13:92010400-92013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:92010400-92021400	Weak transcription	HMEC	breast
33	chr13:92010600-92021200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:92010800-92015200	Weak transcription	Fetal Intestine Small	intestine
35	chr13:92010800-92020800	Weak transcription	HSMM	muscle
36	chr13:92010800-92021000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:92010800-92021000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:92010800-92021200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr13:92010800-92021200	Weak transcription	HUVEC	blood vessel
40	chr13:92010800-92026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:92011000-92013800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr13:92011000-92017200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:92011000-92021000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr13:92011000-92021000	Weak transcription	Psoas Muscle	Psoas
45	chr13:92011000-92021200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr13:92011400-92020600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:92011800-92013600	Enhancers	A549	lung
48	chr13:92011800-92016400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:92011800-92020600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:92011800-92020600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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