Variant report

Variant	rs6043624
Chromosome Location	chr20:15911324-15911325
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	RAD21	chr20:15910853-15911406	MCF-7	breast:	n/a	chr20:15911120-15911139
2	RAD21	chr20:15910857-15911456	H1-hESC	embryonic stem cell:	n/a	chr20:15911120-15911139
3	TCF7L2	chr20:15911049-15911872	Hela-S3	cervix:	n/a	chr20:15911636-15911643
4	RAD21	chr20:15910874-15911385	A549	lung:	n/a	chr20:15911120-15911139
5	RAD21	chr20:15910861-15911383	ECC-1	luminal epithelium:	n/a	chr20:15911120-15911139
6	RAD21	chr20:15910910-15911343	IMR90	lung:	n/a	chr20:15911120-15911139
7	CTCF	chr20:15910922-15911326	IMR90	lung:	n/a	chr20:15911122-15911140 chr20:15911128-15911137 chr20:15911117-15911138
8	RAD21	chr20:15910733-15911426	MCF-7	breast:	n/a	chr20:15911120-15911139
9	RAD21	chr20:15910890-15911328	SK-N-SH_RA	brain:	n/a	chr20:15911120-15911139
10	RAD21	chr20:15910726-15912155	SK-N-SH	brain:	n/a	chr20:15911120-15911139
11	RAD21	chr20:15910829-15911385	A549	lung:	n/a	chr20:15911120-15911139
12	CTCF	chr20:15910939-15911338	A549	lung:	n/a	chr20:15911122-15911140 chr20:15911128-15911137 chr20:15911117-15911138
13	RAD21	chr20:15910890-15911373	H1-hESC	embryonic stem cell:	n/a	chr20:15911120-15911139
14	RAD21	chr20:15910915-15911334	H1-hESC	embryonic stem cell:	n/a	chr20:15911120-15911139
15	CTCF	chr20:15911320-15911470	AG04449	skin:	n/a	n/a
16	RAD21	chr20:15910887-15911356	ECC-1	luminal epithelium:	n/a	chr20:15911120-15911139
17	CTCF	chr20:15910894-15911382	MCF-7	breast:	n/a	chr20:15911122-15911140 chr20:15911128-15911137 chr20:15911117-15911138
18	CTCF	chr20:15910895-15911333	HepG2	liver:	n/a	chr20:15911122-15911140 chr20:15911128-15911137 chr20:15911117-15911138
19	RAD21	chr20:15910892-15911340	HepG2	liver:	n/a	chr20:15911120-15911139
20	CTCF	chr20:15910783-15911953	A549	lung:	n/a	chr20:15911122-15911140 chr20:15911128-15911137 chr20:15911117-15911138
21	RAD21	chr20:15910901-15911986	Hela-S3	cervix:	n/a	chr20:15911120-15911139
22	MYC	chr20:15911018-15911978	MCF10A-Er-Src	breast:	n/a	n/a
23	SMC3	chr20:15910943-15911940	Hela-S3	cervix:	n/a	chr20:15911124-15911138
24	CEBPB	chr20:15910925-15911974	Hela-S3	cervix:	n/a	chr20:15911671-15911682
25	SMC3	chr20:15910723-15911603	SK-N-SH	brain:	n/a	chr20:15911124-15911138
26	CTCF	chr20:15911180-15911330	HAc	cerebellar:	n/a	n/a
27	RCOR1	chr20:15911038-15911881	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr20:15910725-15911482	SK-N-SH	brain:	n/a	chr20:15911122-15911140 chr20:15911128-15911137 chr20:15911117-15911138

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:15823268..15824166-chr20:15910502..15911549,3	MCF-7	breast:

Variant related genes	Relation type
MACROD2	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1339255	1.00[CEU][hapmap]
rs175780	1.00[CEU][hapmap]
rs2143550	1.00[CEU][hapmap]
rs2423987	1.00[CEU][hapmap]
rs4814418	1.00[CEU][hapmap]
rs4814421	1.00[CEU][hapmap]
rs6034327	0.96[ASN][1000 genomes]
rs6034328	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6034330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034337	1.00[CEU][hapmap]
rs6043602	1.00[CEU][hapmap]
rs6043620	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6043627	1.00[CEU][hapmap]
rs6043632	1.00[CEU][hapmap]
rs6043638	1.00[CEU][hapmap]
rs6080021	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6080022	1.00[CEU][hapmap]
rs6080023	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6080024	0.82[EUR][1000 genomes]
rs6080048	0.80[ASN][1000 genomes]
rs6080050	0.80[ASN][1000 genomes]
rs6105492	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6110832	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6110836	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6131738	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6135612	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs717146	1.00[CEU][hapmap]
rs722337	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7352227	1.00[CEU][hapmap]
rs775094	1.00[CEU][hapmap]
rs775096	1.00[CEU][hapmap]
rs811343	1.00[CEU][hapmap]
rs9967921	0.91[EUR][1000 genomes];0.93[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	nsv869328	chr20:15325423-16213898	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv833929	chr20:15765372-15977337	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3447866	chr20:15799286-16115291	Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:15884400-15917400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:15904800-15916200	Weak transcription	GM12878-XiMat	blood
3	chr20:15910600-15911400	Enhancers	Colon Smooth Muscle	Colon
4	chr20:15910800-15911400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:15910800-15911400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr20:15910800-15911400	Active TSS	Brain Substantia Nigra	brain
7	chr20:15910800-15911400	Active TSS	Fetal Brain Female	brain
8	chr20:15910800-15911600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:15910800-15911600	Enhancers	Fetal Heart	heart
10	chr20:15910800-15911600	Enhancers	Fetal Kidney	kidney
11	chr20:15910800-15911800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr20:15910800-15912000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr20:15910800-15912000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr20:15910800-15912000	Enhancers	Fetal Brain Male	brain
15	chr20:15910800-15912200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:15910800-15912200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr20:15910800-15912200	Enhancers	Hela-S3	cervix
18	chr20:15911000-15911800	Enhancers	HSMM	muscle
19	chr20:15911000-15912000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr20:15911000-15912200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr20:15911000-15912200	Enhancers	Primary B cells from peripheral blood	blood
22	chr20:15911200-15911400	Enhancers	Spleen	Spleen
23	chr20:15911200-15911600	Weak transcription	Primary B cells from cord blood	blood
24	chr20:15911200-15911600	Enhancers	Brain Hippocampus Middle	brain
25	chr20:15911200-15911800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr20:15911200-15912200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:15911200-15912200	Enhancers	Adipose Nuclei	Adipose
28	chr20:15911200-15912200	Enhancers	Fetal Intestine Small	intestine
29	chr20:15911200-15912400	Enhancers	HMEC	breast

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