Variant report

Variant	rs3822754
Chromosome Location	chr5:95117215-95117216
allele	A/C
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	FOXM1	chr5:95116628-95117337	GM12878	blood:	n/a	n/a
2	CTCF	chr5:95116481-95117460	A549	lung:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
3	SMC3	chr5:95116460-95117297	HepG2	liver:	n/a	chr5:95116912-95116919 chr5:95116912-95116926
4	RAD21	chr5:95116491-95117355	HCT-116	colon:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
5	CTCF	chr5:95116510-95117383	HCT-116	colon:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
6	RAD21	chr5:95116551-95117304	HepG2	liver:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
7	SMC3	chr5:95116575-95117307	Hela-S3	cervix:	n/a	chr5:95116912-95116919 chr5:95116912-95116926
8	RAD21	chr5:95116621-95117260	Hela-S3	cervix:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
9	SMC3	chr5:95116515-95117314	GM12878	blood:	n/a	chr5:95116912-95116919 chr5:95116912-95116926
10	CTCF	chr5:95117115-95117282	GM10248	blood:	n/a	n/a
11	CTCF	chr5:95116644-95117381	HCT-116	colon:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
12	CTCF	chr5:95116648-95117337	K562	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
13	CTCF	chr5:95116778-95117224	K562	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
14	RAD21	chr5:95116636-95117225	IMR90	lung:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
15	CTCF	chr5:95116777-95117224	GM12878	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
16	CTCF	chr5:95116771-95117299	GM10266	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
17	RAD21	chr5:95116560-95117399	HCT-116	colon:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
18	RAD21	chr5:95116713-95117281	SK-N-SH_RA	brain:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
19	CTCF	chr5:95116753-95117273	A549	lung:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
20	ARID3A	chr5:95116851-95117250	K562	blood:	n/a	n/a
21	RAD21	chr5:95116683-95117242	ECC-1	luminal epithelium:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
22	CTCF	chr5:95116680-95117325	GM12878	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
23	BCLAF1	chr5:95116679-95117229	GM12878	blood:	n/a	n/a
24	CTCF	chr5:95116656-95117337	HepG2	liver:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
25	CTCF	chr5:95115757-95117524	SK-N-SH	brain:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
26	RAD21	chr5:95116594-95117227	H1-hESC	embryonic stem cell:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
27	MAX	chr5:95116646-95117223	A549	lung:	n/a	n/a
28	CTCF	chr5:95116736-95117334	Spleen_OC	spleen:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
29	POLR2A	chr5:95101625-95118213	K562	blood:	n/a	n/a
30	RAD21	chr5:95116656-95117237	SK-N-SH_RA	brain:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
31	ZNF143	chr5:95116729-95117291	GM12878	blood:	n/a	n/a
32	RAD21	chr5:95116679-95117316	A549	lung:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
33	POLR2A	chr5:95111953-95118472	MCF-7	breast:	n/a	n/a
34	CTCF	chr5:95116646-95117346	K562	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
35	RAD21	chr5:95116736-95117222	MCF-7	breast:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
36	TCF12	chr5:95116659-95117277	A549	lung:	n/a	n/a
37	RAD21	chr5:95116693-95117265	H1-hESC	embryonic stem cell:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
38	CTCF	chr5:95116606-95117323	A549	lung:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
39	CTCF	chr5:95116785-95117276	LNCaP	prostate:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
40	CTCF	chr5:95116577-95117318	IMR90	lung:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
41	CTCF	chr5:95116710-95117250	HepG2	liver:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
42	CTCF	chr5:95116795-95117254	LNCaP	prostate:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
43	RAD21	chr5:95116606-95117383	A549	lung:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
44	CTCF	chr5:95116781-95117259	K562	blood:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
45	CTCF	chr5:95116668-95117321	MCF-7	breast:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
46	CTCF	chr5:95116681-95117247	ECC-1	luminal epithelium:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
47	CTCF	chr5:95116784-95117247	HUVEC	blood vessel:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
48	POLR2A	chr5:95116863-95118080	K562	blood:	n/a	n/a
49	RAD21	chr5:95116653-95117325	GM12878	blood:	n/a	chr5:95116914-95116927 chr5:95116911-95116930
50	CTCF	chr5:95116777-95117215	Medullo	brain:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933

No.	Distal block	Cell Line	Cell type
1	chr5:94999575..95000363-chr5:95116659..95117611,3	MCF-7	breast:
2	chr5:95116606..95117631-chr5:95177527..95180416,16	MCF-7	breast:
3	chr5:95116750..95117321-chr5:95178501..95179151,2	MCF-7	breast:
4	chr5:95116312..95117533-chr5:95181736..95183486,9	MCF-7	breast:
5	chr5:94979766..94982277-chr5:95116115..95117894,2	MCF-7	breast:
6	chr5:95116701..95117451-chr5:95170394..95171284,4	MCF-7	breast:
7	chr5:95115987..95117779-chr5:95182285..95183519,12	K562	blood:
8	chr5:94999582..95000479-chr5:95116324..95117450,4	K562	blood:
9	chr5:95116455..95117958-chr5:95120656..95123513,2	K562	blood:
10	chr5:95116503..95117410-chr5:95671774..95672697,3	K562	blood:
11	chr5:95116355..95117924-chr5:95182403..95183379,13	MCF-7	breast:
12	chr5:95115747..95117608-chr5:95119159..95121512,2	MCF-7	breast:

Variant related genes	Relation type
RHOBTB3	TF binding region
ENSG00000164292	Chromatin interaction
ENSG00000251000	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10057261	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10476659	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13170826	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs3756706	0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3777212	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3822753	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[ASN][1000 genomes]
rs6556880	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs6871090	0.89[ASN][1000 genomes]
rs6890561	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7713460	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9314154	1.00[ASN][1000 genomes]
rs9314155	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3822754	POU5F2	cis	parietal	SCAN
rs3822754	GLRX	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95072800-95133400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:95083200-95122000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:95087800-95134000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:95096400-95125400	Weak transcription	Small Intestine	intestine
5	chr5:95096600-95129800	Weak transcription	Colonic Mucosa	Colon
6	chr5:95105000-95131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:95105600-95119200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:95105600-95119800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:95105800-95119400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:95105800-95119400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:95105800-95119600	Weak transcription	Brain Germinal Matrix	brain
12	chr5:95105800-95122200	Weak transcription	Fetal Brain Female	brain
13	chr5:95106400-95127400	Weak transcription	Fetal Brain Male	brain
14	chr5:95107200-95122400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:95109600-95120400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:95109600-95123800	Weak transcription	HepG2	liver
17	chr5:95110400-95120200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:95111800-95117400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:95111800-95120800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:95112200-95118200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr5:95114400-95117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:95114400-95118400	Genic enhancers	Placenta	Placenta
23	chr5:95114800-95117400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr5:95115000-95130200	Strong transcription	K562	blood
25	chr5:95115200-95121400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:95115400-95117400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:95115400-95117400	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr5:95115400-95120400	Weak transcription	Psoas Muscle	Psoas
29	chr5:95115400-95120400	Weak transcription	Right Ventricle	heart
30	chr5:95115400-95123800	Weak transcription	Brain Substantia Nigra	brain
31	chr5:95115400-95127600	Weak transcription	Lung	lung
32	chr5:95115400-95127600	Weak transcription	Spleen	Spleen
33	chr5:95115400-95129400	Weak transcription	Pancreas	Pancrea
34	chr5:95115400-95137800	Weak transcription	Right Atrium	heart
35	chr5:95115400-95138600	Weak transcription	Gastric	stomach
36	chr5:95115400-95139000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr5:95115400-95157000	Weak transcription	Aorta	Aorta
38	chr5:95115600-95117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:95115600-95119400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:95115600-95119400	Weak transcription	Fetal Lung	lung
41	chr5:95115600-95119400	Weak transcription	NH-A	brain
42	chr5:95115600-95134000	Strong transcription	HSMM	muscle
43	chr5:95115800-95133800	Weak transcription	HUVEC	blood vessel
44	chr5:95116200-95117400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:95116200-95117400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr5:95116200-95118200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr5:95116200-95121000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:95116400-95117400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr5:95116400-95117600	Enhancers	Liver	Liver
50	chr5:95116400-95118200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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