Variant report

Variant	rs28362653
Chromosome Location	chr5:36151849-36151850
allele	A/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	NRF1	chr5:36151811-36152704	GM12878	blood:	n/a	chr5:36152281-36152290 chr5:36151998-36152007
2	TAF1	chr5:36151084-36152398	H1-neurons	neurons:	n/a	n/a
3	JUND	chr5:36150843-36152639	K562	blood:	n/a	chr5:36152244-36152255
4	MXI1	chr5:36151200-36152959	H1-hESC	embryonic stem cell:	n/a	chr5:36152713-36152728
5	SIN3AK20	chr5:36151830-36152346	K562	blood:	n/a	n/a
6	POLR2A	chr5:36151614-36152557	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr5:36151821-36152619	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr5:36150838-36153124	K562	blood:	n/a	chr5:36151652-36151663
9	PAX5	chr5:36151730-36152307	GM12892	blood:	n/a	n/a
10	POLR2A	chr5:36151000-36152774	H1-neurons	neurons:	n/a	n/a
11	TAF1	chr5:36151568-36152388	K562	blood:	n/a	n/a
12	YY1	chr5:36151793-36152364	SK-N-SH_RA	brain:	n/a	chr5:36151859-36151873
13	POLR2A	chr5:36150977-36152633	K562	blood:	n/a	n/a
14	TAL1	chr5:36151841-36152437	K562	blood:	n/a	n/a
15	POLR2A	chr5:36151803-36152457	K562	blood:	n/a	n/a
16	POLR2A	chr5:36151749-36152529	A549	lung:	n/a	n/a
17	ETS1	chr5:36151508-36152359	K562	blood:	n/a	chr5:36152139-36152152
18	TAF1	chr5:36151737-36152071	GM12891	blood:	n/a	n/a
19	SIN3AK20	chr5:36151766-36152205	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:36151770-36152437	SK-N-SH	brain:	n/a	n/a
21	GABPA	chr5:36151732-36152456	MCF-7	breast:	n/a	chr5:36152281-36152290 chr5:36151998-36152007
22	TCF12	chr5:36151632-36152603	ECC-1	luminal epithelium:	n/a	n/a
23	REST	chr5:36151828-36152170	SK-N-SH	brain:	n/a	chr5:36151833-36151840 chr5:36151906-36151913
24	CHD2	chr5:36151094-36152465	GM12878	blood:	n/a	n/a
25	SIN3AK20	chr5:36150801-36152866	MCF-7	breast:	n/a	n/a
26	POLR2A	chr5:36151656-36152596	U87	brain:	n/a	n/a
27	STAT1	chr5:36151575-36152515	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:36151759-36152661	MCF10A-Er-Src	breast:	n/a	n/a
29	MAX	chr5:36151213-36152542	A549	lung:	n/a	chr5:36151652-36151663
30	YY1	chr5:36151156-36152399	K562	blood:	n/a	chr5:36151859-36151873 chr5:36151708-36151719
31	POLR2A	chr5:36151593-36152599	MCF-7	breast:	n/a	n/a
32	ATF3	chr5:36151706-36152360	K562	blood:	n/a	n/a
33	YY1	chr5:36151793-36152393	SK-N-SH_RA	brain:	n/a	chr5:36151859-36151873
34	ELF1	chr5:36151153-36152472	GM12878	blood:	n/a	chr5:36152005-36152014 chr5:36151861-36151873
35	CTCF	chr5:36151760-36151910	GM12869	blood:	n/a	n/a
36	CREB1	chr5:36151668-36152480	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:36150424-36152426	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:36151784-36152398	HepG2	liver:	n/a	n/a
39	ARID3A	chr5:36151808-36152340	HepG2	liver:	n/a	n/a
40	SIX5	chr5:36151730-36152513	A549	lung:	n/a	chr5:36152142-36152151 chr5:36152138-36152152 chr5:36152140-36152149
41	POLR2A	chr5:36151685-36152489	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr5:36151735-36152543	Gliobla	brain:	n/a	n/a
43	SP1	chr5:36151841-36152376	GM12878	blood:	n/a	n/a
44	KAT2A	chr5:36151836-36152713	Hela-S3	cervix:	n/a	n/a
45	MXI1	chr5:36151009-36152842	GM12878	blood:	n/a	chr5:36152713-36152728
46	MXI1	chr5:36150616-36153479	IMR90	lung:	n/a	chr5:36152713-36152728
47	E2F6	chr5:36151181-36152620	K562	blood:	n/a	chr5:36152286-36152294 chr5:36152283-36152294 chr5:36152285-36152295 chr5:36152287-36152294 chr5:36152284-36152295 chr5:36152286-36152294
48	SIN3AK20	chr5:36151193-36152370	PANC-1	pancreas:	n/a	n/a
49	ELF1	chr5:36151494-36152374	K562	blood:	n/a	chr5:36152005-36152014 chr5:36151861-36151873
50	TAF1	chr5:36151674-36152364	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:16770619..16771128-chr5:36151289..36152089,2	Hela-S3	cervix:
2	chr1:205718843..205719712-chr5:36151292..36152216,2	Hela-S3	cervix:
3	chr5:36150467..36154483-chr5:36238242..36244873,13	K562	blood:
4	chr5:36114529..36117143-chr5:36150677..36152194,2	K562	blood:
5	chr5:36151113..36153475-chr5:36154153..36156176,2	MCF-7	breast:
6	chr5:36142364..36144449-chr5:36149144..36153081,4	MCF-7	breast:
7	chr2:88927273..88927784-chr5:36151578..36152279,2	Hela-S3	cervix:
8	chr5:36151811..36152410-chr5:43603002..43603620,2	Hela-S3	cervix:
9	chr5:36141299..36144114-chr5:36149805..36153077,4	K562	blood:
10	chr5:36114529..36117143-chr5:36150539..36152194,3	K562	blood:
11	chr5:36150277..36153703-chr5:36154371..36162094,13	K562	blood:
12	chr5:36150463..36155255-chr5:36239958..36244873,10	K562	blood:
13	chr1:116518821..116519420-chr5:36151568..36152447,2	Hela-S3	cervix:
14	chr12:50794755..50795359-chr5:36151589..36152450,2	Hela-S3	cervix:
15	chr5:36149758..36152986-chr5:36154099..36157491,3	MCF-7	breast:

Variant related genes	Relation type
SKP2	TF binding region
MIR580	TF binding region
RNU6-1305P	TF binding region
ENSG00000201223	Chromatin interaction
ENSG00000234028	Chromatin interaction
ENSG00000268790	Chromatin interaction
ENSG00000152620	Chromatin interaction
ENSG00000163393	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000214046	Chromatin interaction
ENSG00000248092	Chromatin interaction
ENSG00000164187	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000069275	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10512648	0.95[ASN][1000 genomes]
rs10941274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655033	0.95[ASN][1000 genomes]
rs12655052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655301	0.83[ASN][1000 genomes]
rs12657634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16902727	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2270909	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs267786	0.85[ASN][1000 genomes]
rs267790	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28362652	0.95[ASN][1000 genomes]
rs35071851	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35708472	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4869463	0.83[ASN][1000 genomes]
rs4869465	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4869615	0.84[AMR][1000 genomes]
rs71617744	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28362653	ENSG00000164187	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36148600-36154600	Active TSS	GM12878-XiMat	blood
2	chr5:36150400-36153400	Active TSS	K562	blood
3	chr5:36150600-36152800	Active TSS	Stomach Smooth Muscle	stomach
4	chr5:36150600-36153400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr5:36150600-36153600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:36150600-36154000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr5:36150800-36152800	Active TSS	Right Ventricle	heart
8	chr5:36150800-36153000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr5:36150800-36153000	Active TSS	Aorta	Aorta
10	chr5:36150800-36153200	Active TSS	Colonic Mucosa	Colon
11	chr5:36150800-36153400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr5:36150800-36153400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:36150800-36153400	Active TSS	Fetal Intestine Large	intestine
14	chr5:36150800-36153400	Active TSS	Fetal Thymus	thymus
15	chr5:36150800-36153400	Active TSS	NHDF-Ad	bronchial
16	chr5:36150800-36153600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr5:36150800-36153600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:36150800-36153600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:36150800-36153600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:36150800-36153600	Active TSS	Psoas Muscle	Psoas
21	chr5:36150800-36153800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr5:36150800-36153800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:36150800-36153800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:36151000-36152400	Active TSS	Thymus	Thymus
25	chr5:36151000-36152600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr5:36151000-36152600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:36151000-36152600	Active TSS	Colon Smooth Muscle	Colon
28	chr5:36151000-36152600	Bivalent/Poised TSS	HepG2	liver
29	chr5:36151000-36152800	Active TSS	Fetal Muscle Leg	muscle
30	chr5:36151000-36152800	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr5:36151000-36152800	Active TSS	Stomach Mucosa	stomach
32	chr5:36151000-36153000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr5:36151000-36153000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:36151000-36153000	Active TSS	Esophagus	oesophagus
35	chr5:36151000-36153000	Active TSS	Left Ventricle	heart
36	chr5:36151000-36153000	Active TSS	Ovary	ovary
37	chr5:36151000-36153000	Active TSS	Pancreas	Pancrea
38	chr5:36151000-36153000	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr5:36151000-36153000	Active TSS	HSMM	muscle
40	chr5:36151000-36153000	Active TSS	Osteobl	bone
41	chr5:36151000-36153200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:36151000-36153200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:36151000-36153200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:36151000-36153200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:36151000-36153200	Active TSS	Fetal Intestine Small	intestine
46	chr5:36151000-36153200	Active TSS	Lung	lung
47	chr5:36151000-36153400	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr5:36151000-36153400	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr5:36151000-36153400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr5:36151000-36153400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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