Variant report

Variant	rs6515306
Chromosome Location	chr20:23146114-23146115
allele	C/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	CTCF	chr20:23145871-23146195	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr20:23145851-23146168	H1-hESC	embryonic stem cell:	n/a	chr20:23146009-23146016
3	CTCF	chr20:23145837-23146205	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr20:23146060-23146210	HEK293	kidney:	n/a	n/a
5	CTCF	chr20:23145837-23146164	K562	blood:	n/a	n/a
6	MAX	chr20:23145854-23146214	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr20:23145795-23146219	H1-hESC	embryonic stem cell:	n/a	chr20:23146009-23146016
8	CTCF	chr20:23145918-23146114	MCF-7	breast:	n/a	n/a
9	CTCF	chr20:23146020-23146170	HCT-116	colon:	n/a	n/a
10	CTCF	chr20:23145927-23146125	K562	blood:	n/a	n/a
11	RAD21	chr20:23145901-23146133	GM12878	blood:	n/a	chr20:23146009-23146016
12	RAD21	chr20:23145796-23146172	SK-N-SH_RA	brain:	n/a	chr20:23146009-23146016
13	RAD21	chr20:23145908-23146118	K562	blood:	n/a	chr20:23146009-23146016
14	MAX	chr20:23145974-23146262	H1-hESC	embryonic stem cell:	n/a	n/a
15	RAD21	chr20:23145765-23146247	HCT-116	colon:	n/a	chr20:23146009-23146016
16	CTCF	chr20:23145906-23146125	MCF-7	breast:	n/a	n/a
17	USF1	chr20:23146082-23146252	HepG2	liver:	n/a	chr20:23146162-23146173
18	CTCF	chr20:23146000-23146150	HRPEpiC	eye:	n/a	n/a
19	CTCF	chr20:23146020-23146170	NHDF-neo	bronchial:	n/a	n/a
20	CTCF	chr20:23146000-23146150	GM06990	blood:	n/a	n/a
21	RAD21	chr20:23145779-23146197	H1-hESC	embryonic stem cell:	n/a	chr20:23146009-23146016
22	RAD21	chr20:23145772-23146153	HepG2	liver:	n/a	chr20:23146009-23146016
23	RAD21	chr20:23145962-23146137	HepG2	liver:	n/a	chr20:23146009-23146016
24	CTCF	chr20:23146000-23146150	K562	blood:	n/a	n/a
25	MAZ	chr20:23145868-23146129	K562	blood:	n/a	n/a
26	ZNF143	chr20:23145970-23146143	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr20:23146000-23146150	GM12866	blood:	n/a	n/a
28	CTCF	chr20:23145980-23146130	GM12864	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:23145826..23148563-chr20:23157728..23159717,2	MCF-7	breast:
2	chr20:23145677..23147489-chr20:23148679..23151441,2	MCF-7	breast:
3	chr20:23038702..23039550-chr20:23145856..23146435,3	MCF-7	breast:

Variant related genes	Relation type
RNA5SP478	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2404887	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6076033	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6076034	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6083025	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6083026	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515305	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7269765	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758516	chr20:23029404-23173240	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2758789	chr20:23029404-23179604	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1066935	chr20:23123507-23146449	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv912817	chr20:23127661-23240969	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23138400-23146400	Enhancers	Placenta	Placenta
2	chr20:23139400-23146600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr20:23139800-23146400	Enhancers	Fetal Muscle Leg	muscle
4	chr20:23139800-23146600	Enhancers	Stomach Mucosa	stomach
5	chr20:23140400-23146400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr20:23140400-23146600	Enhancers	Rectal Mucosa Donor 29	rectum
7	chr20:23140600-23146200	Enhancers	Colonic Mucosa	Colon
8	chr20:23141200-23146200	Enhancers	Fetal Muscle Trunk	muscle
9	chr20:23142200-23146400	Enhancers	Fetal Stomach	stomach
10	chr20:23142800-23146800	Enhancers	Fetal Intestine Large	intestine
11	chr20:23142800-23148000	Weak transcription	NH-A	brain
12	chr20:23143000-23148000	Weak transcription	NHDF-Ad	bronchial
13	chr20:23143200-23147400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:23143400-23146200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr20:23143400-23148000	Weak transcription	NHEK	skin
16	chr20:23143800-23147400	Weak transcription	Esophagus	oesophagus
17	chr20:23144000-23148400	Weak transcription	Right Atrium	heart
18	chr20:23144000-23150800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr20:23144000-23151000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr20:23144400-23147000	Enhancers	Fetal Intestine Small	intestine
21	chr20:23145000-23146400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr20:23145000-23146400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr20:23145200-23150800	Weak transcription	Lung	lung
24	chr20:23145400-23146400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr20:23145400-23146800	Enhancers	Duodenum Mucosa	Duodenum
26	chr20:23145400-23147800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr20:23145600-23146600	Weak transcription	Small Intestine	intestine
28	chr20:23145800-23146400	Enhancers	Gastric	stomach
29	chr20:23145800-23146600	Enhancers	A549	lung
30	chr20:23146000-23146200	Enhancers	Spleen	Spleen
31	chr20:23146000-23146200	Enhancers	K562	blood
32	chr20:23146000-23146400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr20:23146000-23146400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:23146000-23146400	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr20:23146000-23146400	Enhancers	Fetal Heart	heart
36	chr20:23146000-23147600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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