Variant report

Variant	rs60190258
Chromosome Location	chr5:115893716-115893717
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	chr5:115893376-115893764	Hela-S3	cervix:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
2	FOS	chr5:115893461-115893729	MCF10A-Er-Src	breast:	n/a	n/a
3	RAD21	chr5:115893399-115893748	GM12878	blood:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
4	SMC3	chr5:115893361-115893822	GM12878	blood:	n/a	chr5:115893559-115893573
5	MAFK	chr5:115893472-115893857	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr5:115893375-115893770	ECC-1	luminal epithelium:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
7	RAD21	chr5:115893234-115893909	HCT-116	colon:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
8	ARID3A	chr5:115893407-115893716	HepG2	liver:	n/a	n/a
9	SMC3	chr5:115893357-115893746	HepG2	liver:	n/a	chr5:115893559-115893573
10	SMC3	chr5:115893378-115893738	Hela-S3	cervix:	n/a	chr5:115893559-115893573
11	SMC3	chr5:115893411-115893734	K562	blood:	n/a	chr5:115893559-115893573
12	RAD21	chr5:115893274-115893717	H1-hESC	embryonic stem cell:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
13	RAD21	chr5:115893379-115893756	HepG2	liver:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
14	CUX1	chr5:115893495-115893830	GM12878	blood:	n/a	n/a
15	RAD21	chr5:115893408-115893747	GM12878	blood:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
16	CTCF	chr5:115893580-115893730	HFF	foreskin:	n/a	n/a
17	RAD21	chr5:115893280-115893755	MCF-7	breast:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
18	SMC3	chr5:115893244-115893866	SK-N-SH	brain:	n/a	chr5:115893559-115893573
19	CTCF	chr5:115893428-115893768	HCT-116	colon:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
20	CTCF	chr5:115893373-115893818	K562	blood:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
21	RAD21	chr5:115893304-115893865	HepG2	liver:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
22	RAD21	chr5:115893375-115893765	H1-hESC	embryonic stem cell:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
23	RAD21	chr5:115893243-115893911	A549	lung:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
24	CEBPB	chr5:115893499-115893824	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F4	chr5:115893408-115893815	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr5:115893380-115893745	A549	lung:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
27	RAD21	chr5:115893330-115893753	SK-N-SH_RA	brain:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
28	CTCF	chr5:115893359-115893745	HepG2	liver:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
29	RAD21	chr5:115893428-115893840	A549	lung:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
30	RAD21	chr5:115893367-115893718	HepG2	liver:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
31	CTCF	chr5:115893324-115893736	MCF-7	breast:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
32	RAD21	chr5:115893251-115893879	HCT-116	colon:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
33	CTCF	chr5:115893430-115893749	MCF-7	breast:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
34	RAD21	chr5:115893365-115893800	ECC-1	luminal epithelium:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
35	RAD21	chr5:115893407-115893728	IMR90	lung:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
36	CTCF	chr5:115893267-115893789	HCT-116	colon:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
37	ZNF143	chr5:115893386-115893728	GM12878	blood:	n/a	n/a
38	RAD21	chr5:115893361-115893752	MCF-7	breast:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
39	CUX1	chr5:115893538-115893787	K562	blood:	n/a	n/a
40	RAD21	chr5:115893135-115893846	SK-N-SH	brain:	n/a	chr5:115893562-115893571 chr5:115893563-115893575 chr5:115893561-115893574 chr5:115893558-115893577
41	POLR2A	chr5:115893698-115893723	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr5:115893358-115893790	GM12878	blood:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
43	CTCF	chr5:115893372-115893761	IMR90	lung:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
44	BRCA1	chr5:115893416-115893774	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr5:115893294-115893914	SK-N-SH	brain:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570
46	CTCF	chr5:115893231-115893961	A549	lung:	n/a	chr5:115893484-115893492 chr5:115893559-115893580 chr5:115893558-115893574 chr5:115893557-115893575 chr5:115893562-115893570

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115892597..115894869-chr5:115895299..115897417,2	K562	blood:

Variant related genes	Relation type
ENSG00000239528	TF binding region
SEMA6A	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10037569	1.00[EUR][1000 genomes]
rs10061468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10073342	1.00[EUR][1000 genomes]
rs12332586	1.00[EUR][1000 genomes]
rs13355107	1.00[EUR][1000 genomes]
rs13355323	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13362514	1.00[EUR][1000 genomes]
rs17140058	1.00[EUR][1000 genomes]
rs17140180	1.00[EUR][1000 genomes]
rs28677890	1.00[EUR][1000 genomes]
rs4379240	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58841498	1.00[EUR][1000 genomes]
rs640121	1.00[EUR][1000 genomes]
rs6864548	1.00[EUR][1000 genomes]
rs6897908	1.00[EUR][1000 genomes]
rs73256769	1.00[EUR][1000 genomes]
rs73780329	1.00[EUR][1000 genomes]
rs73780382	1.00[EUR][1000 genomes]
rs7711834	1.00[EUR][1000 genomes]
rs7718743	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3357229	chr5:115893403-115895551	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv2549113	chr5:115893414-115894761	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115880800-115900600	Weak transcription	Fetal Kidney	kidney
2	chr5:115882600-115895400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:115885400-115894000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
4	chr5:115885400-115894600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr5:115886600-115901000	Weak transcription	Placenta	Placenta
6	chr5:115887400-115895000	Weak transcription	Lung	lung
7	chr5:115887400-115897000	Weak transcription	Small Intestine	intestine
8	chr5:115888400-115893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:115889000-115895200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:115889400-115895000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:115889400-115899400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:115889600-115895400	Weak transcription	Fetal Brain Female	brain
13	chr5:115889600-115898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:115890000-115900800	Enhancers	Brain Hippocampus Middle	brain
15	chr5:115890600-115893800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:115890600-115907800	Weak transcription	Spleen	Spleen
17	chr5:115890800-115894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:115890800-115894800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:115890800-115894800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:115890800-115895000	Weak transcription	Left Ventricle	heart
21	chr5:115890800-115895600	Weak transcription	Pancreas	Pancrea
22	chr5:115890800-115895800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:115890800-115898800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:115890800-115907600	Weak transcription	Colonic Mucosa	Colon
25	chr5:115891000-115894200	Enhancers	Brain Anterior Caudate	brain
26	chr5:115891000-115894600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr5:115891000-115894600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:115891000-115894600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:115891000-115895800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr5:115891000-115898200	Weak transcription	Right Atrium	heart
31	chr5:115891000-115900600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:115891000-115907600	Weak transcription	Ovary	ovary
33	chr5:115891200-115904600	Weak transcription	Fetal Stomach	stomach
34	chr5:115891400-115895400	Weak transcription	Psoas Muscle	Psoas
35	chr5:115891400-115905200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:115891800-115894600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr5:115891800-115894800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:115892000-115894800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr5:115892600-115894400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:115892600-115894800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:115893000-115893800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr5:115893000-115894800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:115893000-115894800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:115893000-115894800	Weak transcription	Fetal Intestine Small	intestine
45	chr5:115893200-115893800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr5:115893200-115893800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr5:115893200-115894400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr5:115893200-115894800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:115893200-115895000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:115893200-115895200	Weak transcription	Fetal Muscle Leg	muscle

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