Variant report

Variant	rs319520
Chromosome Location	chr13:93878305-93878306
allele	G/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	KAP1	chr13:93878245-93881236	HEK293	kidney:	n/a	n/a
2	RAD21	chr13:93877927-93883251	SK-N-SH	brain:	n/a	chr13:93879619-93879633 chr13:93879550-93879562 chr13:93879548-93879561 chr13:93879900-93879913 chr13:93879884-93879898 chr13:93880932-93880946
3	MXI1	chr13:93877979-93882972	SK-N-SH	brain:	n/a	n/a
4	FOS	chr13:93877829-93878346	MCF10A-Er-Src	breast:	n/a	chr13:93877987-93877996 chr13:93877987-93877995 chr13:93877988-93877995
5	JUND	chr13:93877878-93879427	H1-hESC	embryonic stem cell:	n/a	chr13:93878983-93878997 chr13:93877987-93877996 chr13:93877985-93877996 chr13:93877987-93877995 chr13:93878667-93878679 chr13:93877988-93877995
6	MXI1	chr13:93878153-93881439	IMR90	lung:	n/a	n/a
7	UBTF	chr13:93878280-93881403	K562	blood:	n/a	n/a
8	BHLHE40	chr13:93877374-93879274	K562	blood:	n/a	n/a
9	MYC	chr13:93878029-93878378	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr13:93877944-93878443	MCF10A-Er-Src	breast:	n/a	chr13:93877986-93877995 chr13:93878420-93878432 chr13:93877987-93877996
11	CEBPB	chr13:93878182-93878349	A549	lung:	n/a	chr13:93878256-93878267
12	CEBPB	chr13:93878005-93878384	H1-hESC	embryonic stem cell:	n/a	chr13:93878256-93878267
13	KAP1	chr13:93877908-93880265	U2OS	brain:	n/a	n/a
14	SIN3A	chr13:93878218-93881230	H1-hESC	embryonic stem cell:	n/a	chr13:93879596-93879609

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:93878289-93878339	PrEC	prostate:	n/a
2	chr13:93878289-93878339	MCF-7	breast:	n/a
3	chr13:93878289-93878339	NHDF-neo	bronchial:	n/a
4	chr13:93878289-93878339	NH-A	brain:	n/a
5	chr13:93878289-93878339	HRPEpiC	eye:	n/a
6	chr13:93878289-93878339	U87	brain:	n/a
7	chr13:93878289-93878339	GM06990	blood:	n/a
8	chr13:93878289-93878339	GM12892	blood:	n/a
9	chr13:93878289-93878339	IMR90	lung:	fetal
10	chr13:93878289-93878339	A549	lung:	n/a
11	chr13:93878289-93878339	SAEC	small airway:	n/a
12	chr13:93878289-93878339	BE2_C	brain:	n/a
13	chr13:93878289-93878339	HAEpiC	amniotic membrane:	n/a
14	chr13:93878289-93878339	HepG2	liver:	n/a
15	chr13:93878289-93878339	AG09319	gingival:	n/a
16	chr13:93878289-93878339	SKMC	muscle:	n/a
17	chr13:93878289-93878339	PFSK-1	brain:	n/a
18	chr13:93878289-93878339	ECC-1	luminal epithelium:	n/a
19	chr13:93878289-93878339	HCM	heart:	n/a
20	chr13:93878289-93878339	K562	blood:	n/a
21	chr13:93878289-93878339	Hepatocyte	liver:	n/a
22	chr13:93878289-93878339	SK-N-MC	brain:	n/a
23	chr13:93878289-93878339	NB4	blood:	n/a
24	chr13:93878289-93878339	LNCaP	prostate:	n/a
25	chr13:93878289-93878339	AoSMC	blood vessel:	n/a
26	chr13:93878289-93878339	ProgFib	skin:	n/a
27	chr13:93878289-93878339	Caco-2	colon:	n/a
28	chr13:93878289-93878339	HUVEC	blood vessel:	n/a
29	chr13:93878289-93878339	CMK	blood:	n/a
30	chr13:93878289-93878339	HNPCEpiC	eye:	n/a
31	chr13:93878289-93878339	ovcar-3	ovarian:	n/a
32	chr13:93878289-93878339	AG04450	lung:	fetal
33	chr13:93878289-93878339	MCF10A-Er-Src	breast:	n/a
34	chr13:93878289-93878339	H1-hESC	embryonic stem cell:	embryo
35	chr13:93878289-93878339	T-47D	breast:	n/a
36	chr13:93878289-93878339	GM12891	blood:	n/a
37	chr13:93878289-93878339	AG10803	skin:	n/a
38	chr13:93878289-93878339	AG04449	skin:	fetal
39	chr13:93878289-93878339	Hela-S3	cervix:	n/a
40	chr13:93878289-93878339	HEEpiC	esophagus:	n/a
41	chr13:93878289-93878339	HEK293	kidney:	embryo
42	chr13:93878289-93878339	HRE	kidney:	n/a
43	chr13:93878289-93878339	AG09309	skin:	n/a
44	chr13:93878289-93878339	HPAEpiC	pulmonary alveolar:	n/a
45	chr13:93878289-93878339	BJ	skin:	n/a
46	chr13:93878289-93878339	SK-N-SH_RA	brain:	n/a
47	chr13:93878289-93878339	HL-60	blood:	n/a
48	chr13:93878289-93878339	HCF	heart:	n/a
49	chr13:93878289-93878339	RPTEC	kidney:	n/a
50	chr13:93878289-93878339	HMEC	breast:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DCT-16	chr13:93876780-93879077	NONHSAT034710

Variant related genes	Relation type
GPC6	TF binding region
GPC6	CpG island

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1413066	0.86[AFR][1000 genomes]
rs1413067	0.86[AFR][1000 genomes]
rs16948474	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1760330	0.86[AFR][1000 genomes]
rs1810933	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1855274	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1855275	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs223307	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2388917	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780374	0.85[AFR][1000 genomes]
rs2780381	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780382	1.00[ASW][hapmap];0.89[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2781035	0.86[AFR][1000 genomes]
rs2781051	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2781052	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319517	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs319518	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319521	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320070	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320071	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320072	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs320075	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320076	1.00[ASW][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320078	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320079	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320080	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320081	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs364631	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs366378	0.84[AFR][1000 genomes]
rs367924	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368555	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs371381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs372160	0.86[AFR][1000 genomes]
rs374389	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs376830	0.83[LWK][hapmap];0.91[MKK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs376851	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs380416	0.86[AFR][1000 genomes]
rs380786	0.86[AFR][1000 genomes]
rs381662	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs385054	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs387992	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs389587	0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs390904	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs394973	0.86[AFR][1000 genomes]
rs397442	1.00[AMR][1000 genomes]
rs415326	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs417537	0.83[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs417815	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs418948	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs420913	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs421381	0.82[AFR][1000 genomes]
rs421861	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs425257	0.86[AFR][1000 genomes]
rs425955	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426342	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426397	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426787	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs427399	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs427409	0.86[AFR][1000 genomes]
rs427503	0.86[AFR][1000 genomes]
rs428015	0.80[YRI][hapmap];0.86[AFR][1000 genomes]
rs4300492	0.82[AFR][1000 genomes]
rs431476	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432632	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432800	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs433129	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs433135	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437703	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437913	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs438139	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs439216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs443603	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs444365	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs448518	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs450509	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs450732	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs451048	0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs454092	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475566	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs489911	0.86[AFR][1000 genomes]
rs489934	0.86[AFR][1000 genomes]
rs521884	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs549385	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7330458	0.86[AFR][1000 genomes]
rs914865	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs914866	0.84[AFR][1000 genomes];1.00[AMR][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	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93871200-93878400	Weak transcription	Fetal Brain Female	brain
2	chr13:93875800-93878400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:93876600-93878400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:93876600-93878400	Enhancers	Fetal Intestine Small	intestine
5	chr13:93876600-93878600	Weak transcription	NHDF-Ad	bronchial
6	chr13:93876600-93878800	Flanking Active TSS	Liver	Liver
7	chr13:93876800-93878400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:93876800-93878400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:93876800-93878400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr13:93876800-93878400	Enhancers	Fetal Intestine Large	intestine
11	chr13:93876800-93878600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr13:93876800-93878600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:93876800-93879000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:93876800-93879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:93877000-93878400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:93877000-93878400	Enhancers	HSMMtube	muscle
17	chr13:93877000-93878800	Flanking Active TSS	HepG2	liver
18	chr13:93877000-93879200	Active TSS	A549	lung
19	chr13:93877200-93878400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr13:93877200-93878400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:93877200-93878400	Weak transcription	Fetal Kidney	kidney
22	chr13:93877400-93878400	Enhancers	Muscle Satellite Cultured Cells	--
23	chr13:93877600-93879000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:93877800-93878400	Enhancers	HMEC	breast
25	chr13:93877800-93878800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr13:93878000-93878400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr13:93878000-93878400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:93878000-93878600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr13:93878000-93878600	Enhancers	Brain Germinal Matrix	brain
30	chr13:93878000-93878800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr13:93878000-93878800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:93878000-93878800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:93878000-93878800	Enhancers	Fetal Heart	heart
34	chr13:93878000-93881600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr13:93878000-93882800	Active TSS	Aorta	Aorta
36	chr13:93878200-93878400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr13:93878200-93878400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr13:93878200-93878400	Enhancers	Fetal Stomach	stomach
39	chr13:93878200-93878400	Enhancers	NHEK	skin
40	chr13:93878200-93878600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr13:93878200-93878600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr13:93878200-93878600	Flanking Active TSS	HSMM	muscle
43	chr13:93878200-93878600	Flanking Active TSS	Osteobl	bone
44	chr13:93878200-93878800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:93878200-93878800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:93878200-93878800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr13:93878200-93878800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:93878200-93878800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr13:93878200-93878800	Flanking Active TSS	Fetal Lung	lung
50	chr13:93878200-93878800	Flanking Active TSS	NH-A	brain

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