Variant report

Variant	rs471315
Chromosome Location	chr13:50961493-50961494
allele	C/G
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	RAD21	chr13:50961103-50961568	MCF-7	breast:	n/a	n/a
2	CTCF	chr13:50961262-50961511	MCF-7	breast:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
3	CTCF	chr13:50961197-50961520	GM12878	blood:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
4	CTCF	chr13:50961262-50961504	MCF-7	breast:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
5	CTCF	chr13:50961257-50961522	MCF-7	breast:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
6	RAD21	chr13:50961175-50961527	HepG2	liver:	n/a	n/a
7	CTCF	chr13:50961360-50961510	WI-38	lung:	n/a	n/a
8	CTCF	chr13:50961400-50961550	WI-38	lung:	n/a	n/a
9	CTCF	chr13:50961210-50961559	IMR90	lung:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
10	CTCF	chr13:50961380-50961530	HVMF	connective:	n/a	n/a
11	RCOR1	chr13:50961079-50961526	K562	blood:	n/a	n/a
12	RAD21	chr13:50961147-50961525	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr13:50961282-50961512	GM19239	blood:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
14	RAD21	chr13:50961221-50961580	IMR90	lung:	n/a	n/a
15	CTCF	chr13:50961360-50961510	GM12875	blood:	n/a	n/a
16	RAD21	chr13:50960916-50961544	H1-hESC	embryonic stem cell:	n/a	n/a
17	KAP1	chr13:50960755-50961747	HEK293	kidney:	n/a	n/a
18	RAD21	chr13:50961182-50961508	GM12878	blood:	n/a	n/a
19	RAD21	chr13:50961095-50961539	HepG2	liver:	n/a	n/a
20	CTCF	chr13:50961169-50961572	MCF-7	breast:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
21	CTCF	chr13:50961229-50961568	K562	blood:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
22	RAD21	chr13:50961158-50961493	HepG2	liver:	n/a	n/a
23	CTCF	chr13:50961179-50961536	K562	blood:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
24	SMC3	chr13:50961262-50961513	K562	blood:	n/a	chr13:50961337-50961347
25	RAD21	chr13:50961025-50961687	SK-N-SH	brain:	n/a	n/a
26	HA-E2F1	chr13:50961222-50961676	MCF-7	breast:	n/a	n/a
27	CTCF	chr13:50961227-50961537	H1-hESC	embryonic stem cell:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
28	CTCF	chr13:50961276-50961519	MCF-7	breast:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
29	RCOR1	chr13:50961073-50961555	K562	blood:	n/a	n/a
30	CTCF	chr13:50961380-50961530	HFF-Myc	foreskin:	n/a	n/a
31	BHLHE40	chr13:50961376-50961565	K562	blood:	n/a	n/a
32	KAP1	chr13:50960701-50961798	U2OS	brain:	n/a	n/a
33	SIN3A	chr13:50960747-50961495	H1-hESC	embryonic stem cell:	n/a	chr13:50961070-50961083
34	RAD21	chr13:50961152-50961626	MCF-7	breast:	n/a	n/a
35	RAD21	chr13:50961131-50961577	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr13:50961269-50961502	MCF-7	breast:	n/a	chr13:50961342-50961350 chr13:50961358-50961371 chr13:50961356-50961374
37	RAD21	chr13:50961071-50961622	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr13:50961360-50961510	BJ	skin:	n/a	n/a
39	RAD21	chr13:50961117-50961526	SK-N-SH_RA	brain:	n/a	n/a
40	JUND	chr13:50961217-50961566	K562	blood:	n/a	n/a
41	MAZ	chr13:50961219-50961561	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50891858..50893890-chr13:50960724..50962841,2	K562	blood:

Variant related genes	Relation type
DLEU1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1327644	0.94[JPT][hapmap]
rs17074346	0.88[ASN][1000 genomes]
rs1924372	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1924373	0.87[ASN][1000 genomes]
rs3116625	0.86[ASN][1000 genomes]
rs35824953	0.94[ASN][1000 genomes]
rs56023535	0.87[ASN][1000 genomes]
rs56075206	0.87[ASN][1000 genomes]
rs58633776	0.93[ASN][1000 genomes]
rs61962133	0.87[ASN][1000 genomes]
rs719103	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7327154	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7334326	0.90[ASN][1000 genomes]
rs7983762	0.88[ASN][1000 genomes]
rs7996632	0.88[ASN][1000 genomes]
rs8000329	0.88[ASN][1000 genomes]
rs8000875	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs8000921	0.88[ASN][1000 genomes]
rs9316495	0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs9562962	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9562963	0.89[ASN][1000 genomes]
rs9562964	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9562965	0.94[ASN][1000 genomes]
rs9562966	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9562967	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9562968	0.88[ASN][1000 genomes]
rs9562970	0.88[ASN][1000 genomes]
rs9562972	0.88[ASN][1000 genomes]
rs9562973	0.87[ASN][1000 genomes]
rs9568397	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9568398	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9568399	0.88[ASN][1000 genomes]
rs9568400	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9568401	0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9568402	0.95[ASN][1000 genomes]
rs9568403	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9568404	0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9568405	0.80[CHD][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs9568406	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs9568407	0.88[ASN][1000 genomes]
rs9568408	0.88[ASN][1000 genomes]
rs9568409	0.88[ASN][1000 genomes]
rs9568410	0.85[ASN][1000 genomes]
rs9568412	0.86[ASN][1000 genomes]
rs9568413	0.87[ASN][1000 genomes]
rs9568416	0.84[ASN][1000 genomes]
rs9634832	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9634834	0.88[ASN][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832609	chr13:50946577-51065968	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs471315	TPT1	cis	parietal	SCAN
rs471315	THSD1P1	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50950400-50967200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:50958600-50961800	Enhancers	Thymus	Thymus
3	chr13:50958600-50961800	Enhancers	Dnd41	blood
4	chr13:50958600-50962800	Enhancers	Fetal Thymus	thymus
5	chr13:50959000-50961800	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr13:50959800-50961800	Enhancers	Fetal Kidney	kidney
7	chr13:50959800-50961800	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr13:50959800-50962600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:50959800-50963000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr13:50960000-50961600	Enhancers	Brain Angular Gyrus	brain
11	chr13:50960000-50961600	Enhancers	Fetal Stomach	stomach
12	chr13:50960000-50961600	Flanking Active TSS	HSMMtube	muscle
13	chr13:50960000-50961800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:50960000-50965000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr13:50960200-50961800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr13:50960400-50961600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr13:50960400-50961600	Enhancers	NHDF-Ad	bronchial
18	chr13:50960400-50961800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr13:50960400-50965000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr13:50960600-50961600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr13:50960600-50961800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr13:50960600-50965000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:50960800-50961600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr13:50960800-50961600	Enhancers	Adipose Nuclei	Adipose
25	chr13:50960800-50961600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr13:50960800-50961600	Flanking Active TSS	HSMM	muscle
27	chr13:50960800-50961800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr13:50961000-50961600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr13:50961000-50961600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:50961000-50961600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:50961000-50961600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr13:50961000-50961600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr13:50961000-50961600	Enhancers	Colonic Mucosa	Colon
34	chr13:50961000-50961600	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr13:50961000-50961600	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr13:50961000-50961600	Enhancers	Lung	lung
37	chr13:50961000-50961600	Enhancers	Pancreas	Pancrea
38	chr13:50961000-50961600	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr13:50961000-50961800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr13:50961000-50961800	Enhancers	K562	blood
41	chr13:50961200-50961600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:50961200-50961600	Enhancers	Brain Hippocampus Middle	brain
43	chr13:50961200-50961600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr13:50961200-50961600	Flanking Active TSS	Left Ventricle	heart
45	chr13:50961200-50961600	Flanking Active TSS	Right Atrium	heart
46	chr13:50961200-50961600	Enhancers	Stomach Mucosa	stomach
47	chr13:50961200-50961600	Enhancers	NHLF	lung
48	chr13:50961200-50961800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:50961200-50961800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr13:50961200-50961800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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