Variant report

Variant	rs512861
Chromosome Location	chr5:15500889-15500890
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	SIN3A	chr5:15499664-15501937	H1-hESC	embryonic stem cell:	n/a	chr5:15500416-15500429 chr5:15500559-15500572
2	POLR2A	chr5:15499932-15501283	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr5:15500506-15501163	U87	brain:	n/a	n/a
4	ELF1	chr5:15500526-15500935	GM12878	blood:	n/a	chr5:15500562-15500574
5	PBX3	chr5:15500588-15502042	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr5:15500760-15500910	HUVEC	blood vessel:	n/a	n/a
7	TBP	chr5:15499682-15500953	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr5:15500819-15500990	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr5:15499923-15500911	HUVEC	blood vessel:	n/a	n/a
10	RAD21	chr5:15499731-15501975	IMR90	lung:	n/a	chr5:15501643-15501650 chr5:15501212-15501222 chr5:15500595-15500614 chr5:15500403-15500416
11	YY1	chr5:15500561-15501228	SK-N-SH_RA	brain:	n/a	chr5:15501151-15501159 chr5:15500775-15500795
12	CTCF	chr5:15500880-15501030	AG04449	skin:	n/a	n/a
13	POLR2A	chr5:15499822-15501110	Gliobla	brain:	n/a	n/a
14	SIN3AK20	chr5:15500549-15501090	SK-N-SH	brain:	n/a	n/a
15	ZNF263	chr5:15499986-15501683	HEK293-T-REx	kidney:	n/a	chr5:15500862-15500871 chr5:15500199-15500208 chr5:15501531-15501540 chr5:15500865-15500886
16	RAD21	chr5:15499982-15500976	H1-hESC	embryonic stem cell:	n/a	chr5:15500595-15500614 chr5:15500403-15500416
17	TAF1	chr5:15500612-15500969	SK-N-SH	brain:	n/a	n/a
18	CTBP2	chr5:15500015-15501869	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr5:15500071-15501140	IMR90	lung:	n/a	n/a
20	POLR2A	chr5:15499665-15501053	HUVEC	blood vessel:	n/a	n/a
21	KAP1	chr5:15500636-15502094	HEK293	kidney:	n/a	chr5:15501836-15501844
22	MAZ	chr5:15499441-15503111	IMR90	lung:	n/a	chr5:15500615-15500625
23	MYC	chr5:15500621-15500952	MCF-7	breast:	n/a	n/a
24	BACH1	chr5:15500629-15500915	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr5:15500840-15500990	WERI-Rb-1	eye:	n/a	n/a
26	POLR2A	chr5:15500003-15501056	ProgFib	skin:	n/a	n/a
27	CTCF	chr5:15500800-15500950	HBMEC	blood vessel:	n/a	n/a
28	POLR2A	chr5:15500632-15500955	H1-neurons	neurons:	n/a	n/a
29	YY1	chr5:15500465-15500929	H1-hESC	embryonic stem cell:	n/a	chr5:15500468-15500477 chr5:15500471-15500480 chr5:15500465-15500479 chr5:15500465-15500474 chr5:15500471-15500485 chr5:15500466-15500477 chr5:15500775-15500795
30	USF2	chr5:15500803-15500938	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr5:15500620-15500965	H1-hESC	embryonic stem cell:	n/a	chr5:15500775-15500795
32	POLR2A	chr5:15500506-15501178	U87	brain:	n/a	n/a
33	POLR2A	chr5:15499671-15501010	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr5:15500555-15500897	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
FBXL7	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10059008	1.00[EUR][1000 genomes]
rs10063263	1.00[EUR][1000 genomes]
rs10077393	1.00[EUR][1000 genomes]
rs11133817	1.00[EUR][1000 genomes]
rs13356380	1.00[EUR][1000 genomes]
rs1529487	1.00[EUR][1000 genomes]
rs16903864	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16903892	1.00[EUR][1000 genomes]
rs188592	1.00[EUR][1000 genomes]
rs2402164	1.00[EUR][1000 genomes]
rs28713425	1.00[EUR][1000 genomes]
rs28716171	1.00[EUR][1000 genomes]
rs2896211	1.00[EUR][1000 genomes]
rs304557	1.00[EUR][1000 genomes]
rs304559	1.00[EUR][1000 genomes]
rs304560	1.00[EUR][1000 genomes]
rs304561	1.00[EUR][1000 genomes]
rs304562	1.00[EUR][1000 genomes]
rs4701626	1.00[EUR][1000 genomes]
rs4701628	1.00[EUR][1000 genomes]
rs4701629	1.00[EUR][1000 genomes]
rs4702074	1.00[EUR][1000 genomes]
rs4702075	1.00[EUR][1000 genomes]
rs4702077	1.00[EUR][1000 genomes]
rs572051	1.00[EUR][1000 genomes]
rs575014	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57991493	1.00[EUR][1000 genomes]
rs598853	1.00[EUR][1000 genomes]
rs609984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs623156	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs629654	0.87[AMR][1000 genomes]
rs633807	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs652985	1.00[EUR][1000 genomes]
rs6554885	1.00[EUR][1000 genomes]
rs683393	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs685706	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751952	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751955	1.00[EUR][1000 genomes]
rs7709371	1.00[EUR][1000 genomes]
rs7717617	1.00[EUR][1000 genomes]
rs9312884	1.00[EUR][1000 genomes]
rs9312886	1.00[EUR][1000 genomes]
rs9968651	1.00[EUR][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	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3345774	chr5:15499527-15501975	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15499400-15501600	Active TSS	Brain Anterior Caudate	brain
2	chr5:15499400-15501800	Active TSS	Brain Hippocampus Middle	brain
3	chr5:15499400-15502200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr5:15499400-15502600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:15499400-15502600	Active TSS	Colon Smooth Muscle	Colon
6	chr5:15499400-15502600	Active TSS	NHDF-Ad	bronchial
7	chr5:15499400-15502800	Active TSS	Brain Substantia Nigra	brain
8	chr5:15499600-15501000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:15499600-15501000	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:15499600-15501600	Active TSS	Placenta Amnion	Placenta Amnion
11	chr5:15499600-15501600	Active TSS	Stomach Smooth Muscle	stomach
12	chr5:15499600-15501800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr5:15499600-15502000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:15499600-15502000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:15499600-15502000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:15499600-15502000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
17	chr5:15499600-15502000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
18	chr5:15499600-15502200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:15499600-15502400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr5:15499600-15502400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr5:15499600-15502400	Active TSS	NH-A	brain
22	chr5:15499600-15502600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:15499600-15502600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:15499600-15502600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:15499600-15502600	Active TSS	Aorta	Aorta
26	chr5:15499600-15502600	Active TSS	Fetal Muscle Trunk	muscle
27	chr5:15499600-15502600	Active TSS	Right Ventricle	heart
28	chr5:15499600-15502800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:15499600-15502800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:15499600-15502800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
31	chr5:15499600-15502800	Active TSS	Fetal Kidney	kidney
32	chr5:15499600-15502800	Active TSS	Left Ventricle	heart
33	chr5:15499600-15502800	Active TSS	Ovary	ovary
34	chr5:15499600-15503000	Active TSS	Right Atrium	heart
35	chr5:15499800-15501000	Bivalent/Poised TSS	Thymus	Thymus
36	chr5:15499800-15501600	Bivalent/Poised TSS	Fetal Thymus	thymus
37	chr5:15499800-15501800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:15499800-15501800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:15499800-15501800	Active TSS	Esophagus	oesophagus
40	chr5:15499800-15501800	Active TSS	Lung	lung
41	chr5:15499800-15502000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:15499800-15502000	Active TSS	Brain Cingulate Gyrus	brain
43	chr5:15499800-15502400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr5:15499800-15502400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:15499800-15502400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr5:15499800-15502600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:15499800-15502600	Active TSS	Brain Angular Gyrus	brain
48	chr5:15499800-15502600	Active TSS	Fetal Stomach	stomach
49	chr5:15499800-15503000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:15500000-15501000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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