Variant report

Variant	rs319521
Chromosome Location	chr13:93878528-93878529
allele	A/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	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	POLR2A	chr13:93878451-93881263	SK-N-MC	brain:	n/a	n/a
4	MXI1	chr13:93877979-93882972	SK-N-SH	brain:	n/a	n/a
5	TBP	chr13:93878495-93879760	HepG2	liver:	n/a	n/a
6	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
7	STAT3	chr13:93878501-93879219	MCF10A-Er-Src	breast:	n/a	chr13:93878739-93878746
8	SP1	chr13:93878437-93879368	A549	lung:	n/a	chr13:93879054-93879068
9	MXI1	chr13:93878153-93881439	IMR90	lung:	n/a	n/a
10	CTCF	chr13:93878385-93881254	SK-N-SH	brain:	n/a	chr13:93880104-93880117 chr13:93879622-93879635
11	FOS	chr13:93878471-93878594	MCF10A-Er-Src	breast:	n/a	n/a
12	CCNT2	chr13:93878338-93881584	K562	blood:	n/a	chr13:93880357-93880366 chr13:93880872-93880892
13	UBTF	chr13:93878280-93881403	K562	blood:	n/a	n/a
14	TBP	chr13:93878335-93879353	K562	blood:	n/a	n/a
15	ZNF263	chr13:93878391-93881322	HEK293-T-REx	kidney:	n/a	n/a
16	POLR2A	chr13:93878366-93881313	HepG2	liver:	n/a	n/a
17	GATA2	chr13:93878470-93881746	SH-SY5Y	brain:	n/a	chr13:93881647-93881654 chr13:93881473-93881489 chr13:93880872-93880889 chr13:93881473-93881489 chr13:93881647-93881654 chr13:93879415-93879425 chr13:93881647-93881654
18	BHLHE40	chr13:93877374-93879274	K562	blood:	n/a	n/a
19	BRCA1	chr13:93878524-93878755	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAZ	chr13:93878377-93879393	K562	blood:	n/a	n/a
21	KAP1	chr13:93877908-93880265	U2OS	brain:	n/a	n/a
22	POLR2A	chr13:93878487-93881295	MCF10A-Er-Src	breast:	n/a	n/a
23	SIN3A	chr13:93878218-93881230	H1-hESC	embryonic stem cell:	n/a	chr13:93879596-93879609
24	ARID3A	chr13:93878382-93879237	HepG2	liver:	n/a	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

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1413066	0.88[AFR][1000 genomes]
rs1413067	0.88[AFR][1000 genomes]
rs16948474	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1760330	0.88[AFR][1000 genomes]
rs1810933	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1855274	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1855275	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs223307	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2388917	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780374	0.86[AFR][1000 genomes]
rs2780381	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2780382	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2781035	0.88[AFR][1000 genomes]
rs2781051	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2781052	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319517	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs319518	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs319520	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320070	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320071	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320072	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs320075	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320076	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320078	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320079	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320080	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs320081	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs364631	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs366378	0.85[AFR][1000 genomes]
rs367924	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs368555	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs371381	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs372160	0.88[AFR][1000 genomes]
rs374389	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs376830	0.90[YRI][hapmap];0.81[AFR][1000 genomes]
rs376851	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs380416	0.88[AFR][1000 genomes]
rs380786	0.88[AFR][1000 genomes]
rs381662	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs385054	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs387992	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs389587	0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs390904	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs394973	0.88[AFR][1000 genomes]
rs397442	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs412938	0.80[AFR][1000 genomes]
rs415326	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs417537	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs417815	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs418948	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs420913	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs421381	0.83[AFR][1000 genomes]
rs421861	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs424491	0.80[AFR][1000 genomes]
rs425257	0.88[AFR][1000 genomes]
rs425955	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426342	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426397	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs426787	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs427399	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs427409	0.88[AFR][1000 genomes]
rs427503	0.88[AFR][1000 genomes]
rs428015	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs4300492	0.83[AFR][1000 genomes]
rs431476	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432632	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs432800	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs433129	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs433135	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437435	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437703	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs437913	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs438139	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs439216	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs443603	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs444365	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs448518	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs450509	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs450732	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs451048	0.91[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs454092	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs475566	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs489911	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs489934	0.88[AFR][1000 genomes]
rs521884	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs549385	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7330458	0.88[AFR][1000 genomes]
rs914865	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs914866	0.85[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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:93876600-93878600	Weak transcription	NHDF-Ad	bronchial
2	chr13:93876600-93878800	Flanking Active TSS	Liver	Liver
3	chr13:93876800-93878600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr13:93876800-93878600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:93876800-93879000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:93876800-93879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:93877000-93878800	Flanking Active TSS	HepG2	liver
8	chr13:93877000-93879200	Active TSS	A549	lung
9	chr13:93877600-93879000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:93877800-93878800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr13:93878000-93878600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr13:93878000-93878600	Enhancers	Brain Germinal Matrix	brain
13	chr13:93878000-93878800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr13:93878000-93878800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:93878000-93878800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:93878000-93878800	Enhancers	Fetal Heart	heart
17	chr13:93878000-93881600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr13:93878000-93882800	Active TSS	Aorta	Aorta
19	chr13:93878200-93878600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr13:93878200-93878600	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr13:93878200-93878600	Flanking Active TSS	HSMM	muscle
22	chr13:93878200-93878600	Flanking Active TSS	Osteobl	bone
23	chr13:93878200-93878800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:93878200-93878800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr13:93878200-93878800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr13:93878200-93878800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:93878200-93878800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr13:93878200-93878800	Flanking Active TSS	Fetal Lung	lung
29	chr13:93878200-93878800	Flanking Active TSS	NH-A	brain
30	chr13:93878200-93879000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
31	chr13:93878200-93879000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:93878200-93879000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr13:93878200-93879000	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr13:93878200-93879200	Active TSS	Right Atrium	heart
35	chr13:93878200-93880600	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr13:93878200-93881000	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr13:93878200-93881600	Active TSS	Colon Smooth Muscle	Colon
38	chr13:93878200-93881600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr13:93878200-93882200	Active TSS	Fetal Brain Male	brain
40	chr13:93878200-93882800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr13:93878400-93878600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr13:93878400-93878600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:93878400-93878600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr13:93878400-93878600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr13:93878400-93878600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr13:93878400-93878600	Enhancers	Brain Angular Gyrus	brain
47	chr13:93878400-93878600	Enhancers	Fetal Brain Female	brain
48	chr13:93878400-93878600	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr13:93878400-93878800	Flanking Active TSS	H9 Cell Line	embryonic stem cell
50	chr13:93878400-93878800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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