Variant report

Variant	rs2731826
Chromosome Location	chr5:94890124-94890125
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	SMARCC1	chr5:94890019-94891663	Hela-S3	cervix:	n/a	chr5:94890827-94890836
2	RCOR1	chr5:94890055-94891259	K562	blood:	n/a	n/a
3	POLR2A	chr5:94890074-94891302	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:94890086-94891297	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr5:94890086-94891331	GM18951	blood:	n/a	n/a
6	MXI1	chr5:94889538-94891614	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:94889973-94891289	GM12891	blood:	n/a	n/a
8	GTF2F1	chr5:94890114-94891431	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:94890039-94891313	HepG2	liver:	n/a	n/a
10	TCF7L2	chr5:94890109-94891341	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr5:94890121-94891299	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:94890121-94891323	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr5:94890108-94891229	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr5:94889417-94891124	K562	blood:	n/a	n/a
15	MAX	chr5:94890114-94891513	NB4	blood:	n/a	n/a
16	MYC	chr5:94890053-94891264	K562	blood:	n/a	n/a
17	ARID3A	chr5:94889972-94891319	K562	blood:	n/a	chr5:94890748-94890764 chr5:94890749-94890765
18	RFX5	chr5:94890015-94891867	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:94889672-94891159	MCF10A-Er-Src	breast:	n/a	n/a
20	TBP	chr5:94890029-94891610	K562	blood:	n/a	n/a
21	MAZ	chr5:94890043-94891611	K562	blood:	n/a	n/a
22	POLR2A	chr5:94890098-94891263	Hela-S3	cervix:	n/a	n/a
23	PML	chr5:94889965-94891352	GM12878	blood:	n/a	n/a
24	SPI1	chr5:94890036-94890368	GM12891	blood:	n/a	chr5:94890186-94890199
25	POLR2A	chr5:94889950-94891349	H1-hESC	embryonic stem cell:	n/a	n/a
26	NRF1	chr5:94890082-94891697	SK-N-SH	brain:	n/a	chr5:94890798-94890807 chr5:94890682-94890696 chr5:94890798-94890809 chr5:94890798-94890809 chr5:94890685-94890694 chr5:94890528-94890537 chr5:94890685-94890696 chr5:94890687-94890696 chr5:94890795-94890809
27	MAX	chr5:94890094-94891356	ECC-1	luminal epithelium:	n/a	n/a
28	IRF1	chr5:94890018-94891785	K562	blood:	n/a	chr5:94890614-94890626 chr5:94890029-94890039 chr5:94890206-94890218 chr5:94891304-94891318 chr5:94891307-94891319 chr5:94891694-94891701 chr5:94890271-94890278
29	MAFK	chr5:94889409-94892087	Hela-S3	cervix:	n/a	chr5:94890316-94890327 chr5:94891579-94891588 chr5:94891579-94891589
30	POLR2A	chr5:94889671-94891602	GM12891	blood:	n/a	n/a
31	JUN	chr5:94889775-94891367	K562	blood:	n/a	n/a
32	FOS	chr5:94890045-94890245	MCF10A-Er-Src	breast:	n/a	n/a
33	EP300	chr5:94889898-94891050	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:94890092-94891336	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr5:94890076-94891257	K562	blood:	n/a	n/a
36	ZNF143	chr5:94890049-94891378	K562	blood:	n/a	chr5:94890818-94890836 chr5:94890827-94890836
37	USF1	chr5:94890121-94891223	HCT-116	colon:	n/a	chr5:94890712-94890721 chr5:94890711-94890720 chr5:94890705-94890726 chr5:94890710-94890721
38	POLR2A	chr5:94890033-94891258	GM12878	blood:	n/a	n/a
39	POLR2A	chr5:94890034-94891076	GM12878	blood:	n/a	n/a
40	SIX5	chr5:94890058-94891420	A549	lung:	n/a	chr5:94890827-94890836
41	TRIM28	chr5:94890081-94891109	K562	blood:	n/a	n/a
42	MXI1	chr5:94889414-94891980	IMR90	lung:	n/a	n/a
43	POLR2A	chr5:94890040-94891277	U87	brain:	n/a	n/a
44	POLR2A	chr5:94889594-94891312	K562	blood:	n/a	n/a
45	RELA	chr5:94890118-94891246	GM10847	blood:	n/a	n/a
46	KAP1	chr5:94890066-94891696	HEK293	kidney:	n/a	n/a
47	POLR2A	chr5:94890095-94891325	K562	blood:	n/a	n/a
48	BRCA1	chr5:94890112-94892024	Hela-S3	cervix:	n/a	n/a
49	RCOR1	chr5:94889461-94891539	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr5:94890087-94891283	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:94890123-94890173	NHDF-neo	bronchial:	n/a
2	chr5:94890123-94890173	PrEC	prostate:	n/a
3	chr5:94890123-94890173	GM06990	blood:	n/a
4	chr5:94890123-94890173	NH-A	brain:	n/a
5	chr5:94890123-94890173	AoSMC	blood vessel:	n/a
6	chr5:94890123-94890173	MCF10A-Er-Src	breast:	n/a
7	chr5:94890123-94890173	Hela-S3	cervix:	n/a
8	chr5:94890123-94890173	U87	brain:	n/a
9	chr5:94890123-94890173	HEEpiC	esophagus:	n/a
10	chr5:94890123-94890173	ProgFib	skin:	n/a
11	chr5:94890123-94890173	BJ	skin:	n/a
12	chr5:94890123-94890173	AG04450	lung:	fetal
13	chr5:94890123-94890173	IMR90	lung:	fetal
14	chr5:94890123-94890173	HRCEpiC	kidney:	n/a
15	chr5:94890123-94890173	GM19239	blood:	n/a
16	chr5:94890123-94890173	CMK	blood:	n/a
17	chr5:94890123-94890173	GM12892	blood:	n/a
18	chr5:94890123-94890173	HAEpiC	amniotic membrane:	n/a
19	chr5:94890123-94890173	Caco-2	colon:	n/a
20	chr5:94890123-94890173	HCT-116	colon:	n/a
21	chr5:94890123-94890173	HEK293	kidney:	embryo
22	chr5:94890123-94890173	PANC-1	pancreas:	n/a
23	chr5:94890123-94890173	HCPEpiC	choroid plexus:	n/a
24	chr5:94890123-94890173	AG09319	gingival:	n/a
25	chr5:94890123-94890173	NT2-D1	testis:	n/a
26	chr5:94890123-94890173	T-47D	breast:	n/a
27	chr5:94890123-94890173	MCF-7	breast:	n/a
28	chr5:94890123-94890173	HCF	heart:	n/a
29	chr5:94890123-94890173	SK-N-SH_RA	brain:	n/a
30	chr5:94890123-94890173	A549	lung:	n/a
31	chr5:94890123-94890173	NB4	blood:	n/a
32	chr5:94890123-94890173	Hepatocyte	liver:	n/a
33	chr5:94890123-94890173	K562	blood:	n/a
34	chr5:94890123-94890173	LNCaP	prostate:	n/a
35	chr5:94890123-94890173	ECC-1	luminal epithelium:	n/a
36	chr5:94890123-94890173	H1-hESC	embryonic stem cell:	embryo
37	chr5:94890123-94890173	HPAEpiC	pulmonary alveolar:	n/a
38	chr5:94890123-94890173	HRE	kidney:	n/a
39	chr5:94890123-94890173	GM12878	blood:	n/a
40	chr5:94890123-94890173	SAEC	small airway:	n/a
41	chr5:94890123-94890173	HRPEpiC	eye:	n/a
42	chr5:94890123-94890173	SK-N-SH	brain:	n/a
43	chr5:94890123-94890173	Jurkat	blood:	n/a
44	chr5:94890123-94890173	RPTEC	kidney:	n/a
45	chr5:94890123-94890173	AG04449	skin:	fetal
46	chr5:94890123-94890173	PFSK-1	brain:	n/a
47	chr5:94890123-94890173	HNPCEpiC	eye:	n/a
48	chr5:94890123-94890173	SKMC	muscle:	n/a
49	chr5:94890123-94890173	AG10803	skin:	n/a
50	chr5:94890123-94890173	HCM	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:94888891..94893786-chr5:94981389..94987516,11	K562	blood:
2	chr5:94889800..94892273-chr5:94955578..94957837,2	MCF-7	breast:
3	chr5:94877399..94880074-chr5:94889020..94891541,2	MCF-7	breast:
4	chr5:94889492..94895025-chr5:94981557..94985063,8	K562	blood:
5	chr5:94885448..94888187-chr5:94888844..94890737,5	K562	blood:
6	chr5:94889331..94891668-chr5:96036859..96038572,2	K562	blood:

Variant related genes	Relation type
ARSK	TF binding region
TTC37	TF binding region
TTC37	CpG island
ARSK	CpG island
ENSG00000175449	Chromatin interaction
ENSG00000153113	Chromatin interaction
ENSG00000178015	Chromatin interaction
ENSG00000198677	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10053324	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10076499	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1183640	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1541798	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981952	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2245588	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255165	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545841	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548652	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2560257	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2560258	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2560260	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2560261	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2560274	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731825	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731833	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2881976	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6556870	0.80[ASN][1000 genomes]
rs73777211	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9314148	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94889000-94890200	Flanking Active TSS	Hela-S3	cervix
2	chr5:94889000-94892200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:94889200-94892000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:94889200-94892000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:94889200-94892800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:94889400-94890200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr5:94889400-94890200	Flanking Active TSS	Colon Smooth Muscle	Colon
8	chr5:94889400-94890200	Flanking Active TSS	Dnd41	blood
9	chr5:94889400-94890400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr5:94889400-94891400	Active TSS	Gastric	stomach
11	chr5:94889400-94891600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:94889400-94891600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:94889400-94891800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:94889400-94891800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:94889400-94891800	Active TSS	Stomach Mucosa	stomach
16	chr5:94889400-94891800	Active TSS	NHLF	lung
17	chr5:94889400-94892000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr5:94889400-94892000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:94889400-94892000	Active TSS	Rectal Smooth Muscle	rectum
20	chr5:94889400-94892200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:94889600-94890200	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr5:94889600-94890200	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr5:94889600-94890200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr5:94889600-94890200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr5:94889600-94890200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr5:94889600-94890200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr5:94889600-94890200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr5:94889600-94890200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:94889600-94890200	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr5:94889600-94890200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:94889600-94890200	Flanking Active TSS	Fetal Brain Male	brain
32	chr5:94889600-94890200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr5:94889600-94890200	Flanking Active TSS	NH-A	brain
34	chr5:94889600-94890200	Flanking Active TSS	Osteobl	bone
35	chr5:94889600-94890400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:94889600-94890400	Flanking Active TSS	Primary B cells from cord blood	blood
37	chr5:94889600-94890400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr5:94889600-94890400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr5:94889600-94890400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:94889600-94890400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr5:94889600-94890400	Flanking Active TSS	Liver	Liver
42	chr5:94889600-94890400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr5:94889600-94890400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr5:94889600-94891400	Active TSS	Lung	lung
45	chr5:94889600-94891600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:94889600-94891600	Active TSS	HSMM	muscle
47	chr5:94889600-94891800	Active TSS	NHEK	skin
48	chr5:94889600-94892000	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr5:94889600-94892000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:94889600-94892000	Active TSS	Right Atrium	heart

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