Variant report

Variant	rs13255178
Chromosome Location	chr8:131417595-131417596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr8:131416739-131417621	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr8:131416797-131417630	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr8:131416745-131417681	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr8:131416523-131417724	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr8:131416675-131417612	SK-N-SH	brain:	n/a	chr8:131417244-131417252
6	EP300	chr8:131416729-131417659	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr8:131416415-131417715	SK-N-SH	brain:	n/a	chr8:131417244-131417252 chr8:131416466-131416476

Variant related genes	Relation type
ASAP1	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10086454	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10086773	0.90[ASN][1000 genomes]
rs10087626	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1008819	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs10090106	0.82[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10090231	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10090767	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10099549	0.86[ASN][1000 genomes]
rs10099586	0.83[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10103132	0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs10107054	0.92[ASN][1000 genomes]
rs10111650	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10956520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10956522	0.86[ASN][1000 genomes]
rs10956523	0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11784638	0.90[ASN][1000 genomes]
rs11992885	0.92[ASN][1000 genomes]
rs11992932	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11992957	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs11993714	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11993741	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11997462	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs12678030	0.86[ASN][1000 genomes]
rs12678808	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12680178	0.86[ASN][1000 genomes]
rs12680697	0.83[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12681664	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13249894	0.92[ASN][1000 genomes]
rs13260346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13275147	0.86[ASN][1000 genomes]
rs13275883	0.81[ASN][1000 genomes]
rs13276168	0.92[ASN][1000 genomes]
rs1340020	0.91[JPT][hapmap]
rs16904260	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16904267	0.90[ASN][1000 genomes]
rs16904268	0.90[ASN][1000 genomes]
rs17215817	0.92[ASN][1000 genomes]
rs17287702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1978551	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs2791349	0.84[CEU][hapmap];0.91[JPT][hapmap]
rs28545757	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28559741	0.82[ASN][1000 genomes]
rs28562521	0.90[ASN][1000 genomes]
rs28707621	0.92[ASN][1000 genomes]
rs28716119	0.92[ASN][1000 genomes]
rs34003529	0.90[ASN][1000 genomes]
rs34019017	0.90[ASN][1000 genomes]
rs34188408	0.86[ASN][1000 genomes]
rs34542318	0.92[ASN][1000 genomes]
rs34676374	0.90[ASN][1000 genomes]
rs34737610	0.92[ASN][1000 genomes]
rs34987314	0.90[ASN][1000 genomes]
rs35123370	0.90[ASN][1000 genomes]
rs35229803	0.81[ASN][1000 genomes]
rs35592532	0.92[ASN][1000 genomes]
rs4504679	0.86[ASN][1000 genomes]
rs4574884	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs4609234	0.89[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs5027392	0.90[ASN][1000 genomes]
rs56677646	0.92[ASN][1000 genomes]
rs6470819	0.85[ASN][1000 genomes]
rs6986119	0.90[ASN][1000 genomes]
rs6986163	0.90[ASN][1000 genomes]
rs6990443	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7014098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7812299	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs7812469	0.84[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7822259	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7822957	0.92[ASN][1000 genomes]
rs7823146	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs7828824	0.92[ASN][1000 genomes]
rs7838650	0.86[ASN][1000 genomes]
rs7844582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9297807	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869334	chr8:131025093-131651487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv915580	chr8:131025093-131667578	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv533085	chr8:131042781-131755007	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs13255178	LEPREL1	trans	lymphoblastoid	seeQTL
rs13255178	LIN7A	trans	lymphoblastoid	seeQTL
rs13255178	FAM171A1	trans	lymphoblastoid	seeQTL
rs13255178	MYO6	trans	lymphoblastoid	seeQTL
rs13255178	PARP12	trans	lymphoblastoid	seeQTL
rs13255178	PLCL2	trans	lymphoblastoid	seeQTL
rs13255178	SLA	cis	cerebellum	SCAN
rs13255178	C1orf106	trans	lymphoblastoid	seeQTL
rs13255178	MNX1	trans	lymphoblastoid	seeQTL
rs13255178	CRIM1	trans	lymphoblastoid	seeQTL
rs13255178	HOXB2	trans	lymphoblastoid	seeQTL
rs13255178	OAS3	trans	lymphoblastoid	seeQTL
rs13255178	KYNU	trans	lymphoblastoid	seeQTL
rs13255178	HNF1B	trans	lymphoblastoid	seeQTL
rs13255178	MFHAS1	trans	lymphoblastoid	seeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:131371600-131419800	Weak transcription	Aorta	Aorta
2	chr8:131395600-131434200	Weak transcription	Hela-S3	cervix
3	chr8:131399400-131419600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:131401600-131421800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:131402600-131418000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr8:131405600-131422800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr8:131405600-131423600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr8:131407400-131419600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr8:131407800-131419400	Weak transcription	Spleen	Spleen
10	chr8:131408000-131422200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr8:131409200-131422400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:131409200-131424000	Weak transcription	Right Ventricle	heart
13	chr8:131409200-131426400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:131409200-131431800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr8:131409400-131421800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr8:131409600-131428400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr8:131410000-131423200	Weak transcription	Adipose Nuclei	Adipose
18	chr8:131410000-131423200	Weak transcription	Ovary	ovary
19	chr8:131411200-131420400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:131411400-131418400	Weak transcription	Fetal Lung	lung
21	chr8:131411400-131419400	Weak transcription	Left Ventricle	heart
22	chr8:131412600-131417600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr8:131414000-131417600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr8:131414400-131431400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:131414600-131419400	Weak transcription	Brain Anterior Caudate	brain
26	chr8:131414600-131422000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr8:131414600-131431000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:131414800-131422000	Weak transcription	Fetal Heart	heart
29	chr8:131415200-131420400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:131416200-131418000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:131416200-131418000	Strong transcription	A549	lung
32	chr8:131416400-131417600	Enhancers	Muscle Satellite Cultured Cells	--
33	chr8:131416400-131418000	Enhancers	Osteobl	bone
34	chr8:131416600-131417600	Enhancers	HSMMtube	muscle
35	chr8:131416600-131418000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr8:131416600-131418000	Enhancers	HSMM	muscle
37	chr8:131416600-131418000	Enhancers	NHDF-Ad	bronchial
38	chr8:131416600-131419600	Genic enhancers	HUVEC	blood vessel
39	chr8:131416600-131420600	Enhancers	NHLF	lung
40	chr8:131416800-131417800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr8:131416800-131418000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr8:131416800-131418000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr8:131416800-131418000	Enhancers	Right Atrium	heart
44	chr8:131416800-131418000	Strong transcription	HepG2	liver
45	chr8:131417000-131417600	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr8:131417000-131417800	Enhancers	Psoas Muscle	Psoas
47	chr8:131417000-131417800	Enhancers	HMEC	breast
48	chr8:131417000-131418000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr8:131417000-131418000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr8:131417000-131418000	Enhancers	Lung	lung

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