Variant report

Variant	rs10152337
Chromosome Location	chr15:45692263-45692264
allele	G/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	chr15:45692220-45692370	HBMEC	blood vessel:	n/a	n/a
2	CTCF	chr15:45692240-45692390	HMEC	breast:	n/a	n/a
3	CTCF	chr15:45691747-45692360	HCT-116	colon:	n/a	chr15:45692002-45692018 chr15:45692006-45692014 chr15:45692001-45692019 chr15:45691996-45692017
4	SMC3	chr15:45691570-45692266	SK-N-SH	brain:	n/a	chr15:45692003-45692017
5	CTCF	chr15:45692240-45692390	GM12878	blood:	n/a	n/a
6	CTCF	chr15:45692238-45692353	GM19238	blood:	n/a	n/a
7	CTCF	chr15:45691814-45692277	HCT-116	colon:	n/a	chr15:45692002-45692018 chr15:45692006-45692014 chr15:45692001-45692019 chr15:45691996-45692017
8	CTCF	chr15:45691562-45692383	A549	lung:	n/a	chr15:45692002-45692018 chr15:45692006-45692014 chr15:45692001-45692019 chr15:45691996-45692017
9	RAD21	chr15:45691719-45692286	A549	lung:	n/a	chr15:45691999-45692018 chr15:45692009-45692016
10	CTCF	chr15:45692240-45692470	AG09319	gingival:	n/a	n/a
11	CTCF	chr15:45692240-45692390	AG10803	skin:	n/a	n/a
12	CTCF	chr15:45692220-45692370	HPAF	blood vessel:	n/a	n/a
13	CTCF	chr15:45691450-45692361	SK-N-SH	brain:	n/a	chr15:45692002-45692018 chr15:45692006-45692014 chr15:45692001-45692019 chr15:45691996-45692017
14	RAD21	chr15:45691798-45692274	MCF-7	breast:	n/a	chr15:45691999-45692018 chr15:45692009-45692016
15	POLR2A	chr15:45691986-45692296	HepG2	liver:	n/a	n/a
16	CTCF	chr15:45692220-45692370	GM12873	blood:	n/a	n/a
17	CTCF	chr15:45692240-45692390	NHDF-neo	bronchial:	n/a	n/a
18	CTCF	chr15:45692220-45692370	GM12867	blood:	n/a	n/a
19	CTCF	chr15:45692240-45692390	GM12874	blood:	n/a	n/a
20	CTCF	chr15:45692240-45692390	AoAF	blood vessel:	n/a	n/a
21	CTCF	chr15:45692240-45692390	AG04449	skin:	n/a	n/a
22	CTCF	chr15:45692220-45692370	HCPEpiC	choroid plexus:	n/a	n/a
23	RAD21	chr15:45691670-45692293	HCT-116	colon:	n/a	chr15:45691999-45692018 chr15:45692009-45692016
24	CTCF	chr15:45692260-45692362	Spleen_OC	spleen:	n/a	n/a
25	RAD21	chr15:45691604-45692281	HCT-116	colon:	n/a	chr15:45691999-45692018 chr15:45692009-45692016
26	CTCF	chr15:45691785-45692264	MCF-7	breast:	n/a	chr15:45692002-45692018 chr15:45692006-45692014 chr15:45692001-45692019 chr15:45691996-45692017
27	RAD21	chr15:45691577-45692321	SK-N-SH	brain:	n/a	chr15:45691999-45692018 chr15:45692009-45692016

No.	Distal block	Cell Line	Cell type
1	chr15:45597883..45600169-chr15:45691864..45693737,3	MCF-7	breast:
2	chr15:45682453..45684162-chr15:45690788..45693416,2	K562	blood:
3	chr11:67112594..67114538-chr15:45691318..45694198,2	MCF-7	breast:
4	chr15:45685120..45688238-chr15:45691728..45694195,3	MCF-7	breast:
5	chr15:45490969..45492554-chr15:45691129..45692848,2	K562	blood:
6	chr15:45598248..45599758-chr15:45691889..45693667,2	MCF-7	breast:
7	chr15:45690046..45692926-chr15:45693483..45695638,2	MCF-7	breast:
8	chr15:45606943..45607901-chr15:45691485..45692421,3	MCF-7	breast:
9	chr15:45601303..45602097-chr15:45691619..45692420,2	MCF-7	breast:

Variant related genes	Relation type
GATM	TF binding region
SPATA5L1	TF binding region
ENSG00000259932	Chromatin interaction
ENSG00000171766	Chromatin interaction
ENSG00000171763	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10152697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12324848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288861	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16942066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1706799	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17533116	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17533716	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17535381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17537244	0.96[ASN][1000 genomes]
rs17618294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433602	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453546	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2461706	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486287	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668746	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55721266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56273246	0.96[ASN][1000 genomes]
rs56306977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56327050	0.96[ASN][1000 genomes]
rs56937414	0.93[ASN][1000 genomes]
rs56967490	0.96[ASN][1000 genomes]
rs57369693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57419781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61301536	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72709081	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709084	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709089	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72709092	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72711253	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711255	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711259	0.96[ASN][1000 genomes]
rs9972405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10152337	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45679000-45693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45682800-45693800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:45685600-45692800	Weak transcription	GM12878-XiMat	blood
4	chr15:45686800-45693600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:45687200-45693800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:45687400-45693200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:45688400-45693400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:45688800-45693600	Weak transcription	Brain Substantia Nigra	brain
9	chr15:45689800-45693200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:45689800-45693200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:45690000-45692600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:45690800-45693200	Enhancers	Liver	Liver
13	chr15:45691400-45693000	Enhancers	HepG2	liver
14	chr15:45691600-45693400	Enhancers	Fetal Intestine Small	intestine
15	chr15:45691800-45693000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:45692000-45693000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:45692000-45693200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:45692000-45693400	Weak transcription	Brain Anterior Caudate	brain
19	chr15:45692000-45693400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr15:45692000-45693400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:45692000-45693400	Weak transcription	Fetal Brain Female	brain
22	chr15:45692000-45693600	Weak transcription	Brain Hippocampus Middle	brain
23	chr15:45692000-45693800	Weak transcription	Small Intestine	intestine
24	chr15:45692200-45692600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:45692200-45693400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:45692200-45693400	Weak transcription	Stomach Mucosa	stomach
27	chr15:45692200-45693600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr15:45692200-45693800	Weak transcription	Pancreas	Pancrea

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