Variant report

Variant	rs8001004
Chromosome Location	chr13:92011832-92011833
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:55)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:55 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr13:92011140..92013314-chr13:92167683..92169572,2	K562	blood:
2	chr13:92007619..92012079-chr13:92329462..92332464,5	K562	blood:
3	chr13:92010635..92015807-chr13:92018550..92023163,4	MCF-7	breast:
4	chr13:81121825..81124571-chr13:92009979..92011924,2	K562	blood:
5	chr13:92010540..92013547-chr13:92187635..92190322,4	K562	blood:
6	chr13:91919276..91922212-chr13:92009101..92012516,4	K562	blood:
7	chr13:92009670..92013881-chr13:92375334..92379387,4	K562	blood:
8	chr13:91926747..91928257-chr13:92010434..92012597,2	K562	blood:
9	chr11:27882879..27884379-chr13:92010659..92012252,2	K562	blood:
10	chr13:90803949..90805680-chr13:92011552..92014384,2	K562	blood:
11	chr13:91795824..91797926-chr13:92010509..92012771,2	K562	blood:
12	chr13:92010191..92014540-chr13:92229897..92231842,4	K562	blood:
13	chr13:91828167..91832824-chr13:92009386..92012550,6	K562	blood:
14	chr13:92008919..92012229-chr13:92298232..92301726,3	K562	blood:
15	chr13:92011718..92012713-chr6:26056548..26057086,2	Hela-S3	cervix:
16	chr13:92010990..92013754-chr13:92321109..92322793,2	K562	blood:
17	chr13:92009199..92012102-chr13:108655339..108657320,2	K562	blood:
18	chr13:91751114..91752648-chr13:92010500..92012399,2	K562	blood:
19	chr13:92006350..92012037-chr13:92182700..92187101,6	K562	blood:
20	chr13:92010436..92012496-chr13:92953050..92954701,2	K562	blood:
21	chr13:91830095..91832824-chr13:92009386..92012550,3	K562	blood:
22	chr13:92011668..92014264-chr13:92248791..92250619,2	K562	blood:
23	chr13:92010929..92013926-chr13:92211896..92214067,2	K562	blood:
24	chr13:92008998..92011983-chr13:92367729..92370311,3	K562	blood:
25	chr13:92009349..92012461-chr13:92224404..92227397,3	K562	blood:
26	chr13:91889138..91891419-chr13:92011620..92013937,2	K562	blood:
27	chr13:91907805..91909994-chr13:92010995..92013406,3	K562	blood:
28	chr13:92011581..92014280-chr13:92377653..92379925,3	K562	blood:
29	chr13:92008212..92012126-chr13:92101857..92105185,4	K562	blood:
30	chr13:92010067..92012640-chr9:133779649..133782513,2	K562	blood:
31	chr13:92009525..92012032-chr13:92219135..92221631,2	K562	blood:
32	chr13:92009508..92013495-chr13:92125822..92129742,3	K562	blood:
33	chr13:91999461..92007353-chr13:92008154..92015149,15	MCF-7	breast:
34	chr13:92011474..92015304-chr13:92379938..92384751,4	K562	blood:
35	chr13:92011441..92013095-chr13:92360368..92362674,2	K562	blood:
36	chr13:92007380..92009324-chr13:92011441..92013491,2	MCF-7	breast:
37	chr13:92010600..92013246-chr13:92212301..92213807,2	K562	blood:
38	chr13:91796426..91798959-chr13:92009042..92012009,2	K562	blood:
39	chr13:92009446..92011873-chr13:92285779..92287489,2	K562	blood:
40	chr13:91692018..91694558-chr13:92011037..92013238,2	K562	blood:
41	chr13:92010398..92013351-chr13:108550982..108553660,2	K562	blood:
42	chr13:92010904..92013459-chr13:92248662..92250979,3	K562	blood:
43	chr13:92009784..92014607-chr13:92111183..92117003,5	K562	blood:
44	chr13:91461776..91463287-chr13:92011640..92013269,2	K562	blood:
45	chr13:92008301..92012941-chr13:92190227..92194060,8	K562	blood:
46	chr13:92009908..92012117-chr2:43452729..43454781,2	K562	blood:
47	chr13:92010706..92013622-chr13:93006752..93008493,2	K562	blood:
48	chr13:91874317..91877708-chr13:92010260..92012794,3	K562	blood:
49	chr13:92011474..92014177-chr13:92380431..92383913,3	K562	blood:
50	chr13:92010873..92012565-chr13:92225020..92227817,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000187837	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000179399	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000152518	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1330062	0.96[ASN][1000 genomes]
rs1330063	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1428	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs4142965	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]
rs4284505	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4773624	1.00[ASN][1000 genomes]
rs4773625	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319045	1.00[ASN][1000 genomes]
rs7319759	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7320878	0.96[CEU][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7322734	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7324173	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336610	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8002779	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs932910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9515919	1.00[ASN][1000 genomes]
rs9523304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9523307	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9523310	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9523312	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9523313	1.00[ASN][1000 genomes]
rs976547	0.83[AMR][1000 genomes];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
rs8001004	GPC5	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:92001600-92012200	Weak transcription	Esophagus	oesophagus
2	chr13:92001800-92015600	Weak transcription	Ovary	ovary
3	chr13:92001800-92027200	Weak transcription	Aorta	Aorta
4	chr13:92002000-92012200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:92002400-92012000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr13:92003400-92014000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:92003600-92012000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr13:92003600-92012600	Weak transcription	Brain Substantia Nigra	brain
9	chr13:92003600-92012800	Weak transcription	Small Intestine	intestine
10	chr13:92003600-92016600	Weak transcription	Gastric	stomach
11	chr13:92003600-92021200	Weak transcription	Right Ventricle	heart
12	chr13:92003600-92033200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:92003800-92012200	Strong transcription	Fetal Thymus	thymus
14	chr13:92003800-92012200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr13:92003800-92012600	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:92004600-92012200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr13:92004600-92021200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr13:92006600-92013400	Weak transcription	NHDF-Ad	bronchial
19	chr13:92007600-92012200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr13:92007800-92012200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:92007800-92015200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:92008400-92014600	Weak transcription	Hela-S3	cervix
23	chr13:92008600-92014000	Weak transcription	Fetal Intestine Large	intestine
24	chr13:92008800-92012000	Genic enhancers	K562	blood
25	chr13:92008800-92013800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:92008800-92021000	Weak transcription	Osteobl	bone
27	chr13:92008800-92021400	Weak transcription	NHLF	lung
28	chr13:92009200-92016200	Enhancers	Liver	Liver
29	chr13:92009400-92014000	Weak transcription	Fetal Lung	lung
30	chr13:92009400-92014000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr13:92009400-92020000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:92009400-92020800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:92009600-92021200	Weak transcription	HSMMtube	muscle
34	chr13:92009600-92022200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:92009800-92012400	Weak transcription	Adipose Nuclei	Adipose
36	chr13:92009800-92012400	Weak transcription	Dnd41	blood
37	chr13:92009800-92014800	Weak transcription	Left Ventricle	heart
38	chr13:92009800-92021200	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr13:92009800-92021200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:92010000-92012200	Weak transcription	Fetal Muscle Leg	muscle
41	chr13:92010000-92012600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr13:92010000-92012800	Weak transcription	NHEK	skin
43	chr13:92010000-92013800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr13:92010000-92014400	Weak transcription	Brain Germinal Matrix	brain
45	chr13:92010000-92014800	Enhancers	HepG2	liver
46	chr13:92010000-92021000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr13:92010000-92021000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr13:92010200-92012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:92010200-92021200	Weak transcription	NH-A	brain
50	chr13:92010200-92021600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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