Variant report

Variant	rs2560277
Chromosome Location	chr5:94890632-94890633
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	ELF1	chr5:94890256-94891245	GM12878	blood:	n/a	chr5:94891162-94891171
2	MYBL2	chr5:94890144-94891141	HepG2	liver:	n/a	n/a
3	MAX	chr5:94890144-94891281	Hela-S3	cervix:	n/a	n/a
4	SMARCC1	chr5:94890019-94891663	Hela-S3	cervix:	n/a	chr5:94890827-94890836
5	USF1	chr5:94890257-94891158	HCT-116	colon:	n/a	chr5:94890712-94890721 chr5:94890711-94890720 chr5:94890705-94890726 chr5:94890710-94890721
6	RCOR1	chr5:94890055-94891259	K562	blood:	n/a	n/a
7	POLR2A	chr5:94890074-94891302	SK-N-SH	brain:	n/a	n/a
8	TAF1	chr5:94890154-94891186	K562	blood:	n/a	n/a
9	POLR2A	chr5:94890086-94891297	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:94890086-94891331	GM18951	blood:	n/a	n/a
11	FOS	chr5:94890588-94890886	MCF10A-Er-Src	breast:	n/a	n/a
12	ZBTB33	chr5:94890434-94890969	A549	lung:	n/a	n/a
13	TCF7L2	chr5:94890253-94891283	PANC-1	pancreas:	n/a	n/a
14	MXI1	chr5:94889538-94891614	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr5:94890149-94891287	GM19193	blood:	n/a	n/a
16	POLR2A	chr5:94889973-94891289	GM12891	blood:	n/a	n/a
17	ZNF143	chr5:94890273-94891305	H1-hESC	embryonic stem cell:	n/a	chr5:94890818-94890836 chr5:94890827-94890836
18	TAF1	chr5:94890553-94890982	Hela-S3	cervix:	n/a	n/a
19	USF1	chr5:94890365-94891014	K562	blood:	n/a	chr5:94890712-94890721 chr5:94890711-94890720 chr5:94890705-94890726 chr5:94890710-94890721
20	MAX	chr5:94890142-94891251	K562	blood:	n/a	n/a
21	SIX5	chr5:94890436-94891029	A549	lung:	n/a	chr5:94890827-94890836
22	TAF1	chr5:94890331-94891289	PFSK-1	brain:	n/a	n/a
23	NFIC	chr5:94890550-94891069	HepG2	liver:	n/a	n/a
24	SIN3AK20	chr5:94890496-94890918	H1-hESC	embryonic stem cell:	n/a	n/a
25	UBTF	chr5:94890205-94891865	K562	blood:	n/a	n/a
26	BRCA1	chr5:94890373-94891243	HepG2	liver:	n/a	n/a
27	POLR2A	chr5:94890395-94891218	HUVEC	blood vessel:	n/a	n/a
28	GTF2F1	chr5:94890114-94891431	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr5:94890039-94891313	HepG2	liver:	n/a	n/a
30	TCF7L2	chr5:94890109-94891341	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr5:94890121-94891299	H1-hESC	embryonic stem cell:	n/a	n/a
32	ELF1	chr5:94890561-94890888	HepG2	liver:	n/a	n/a
33	FOS	chr5:94890571-94890861	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr5:94890121-94891323	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr5:94890150-94891213	GM12878	blood:	n/a	n/a
36	MAX	chr5:94890127-94891363	Hela-S3	cervix:	n/a	n/a
37	NFIC	chr5:94890491-94891028	HepG2	liver:	n/a	n/a
38	POLR2A	chr5:94890108-94891229	Hela-S3	cervix:	n/a	n/a
39	RELA	chr5:94890181-94891321	GM15510	blood:	n/a	n/a
40	TAF1	chr5:94890567-94890998	GM12892	blood:	n/a	n/a
41	POLR2A	chr5:94890268-94891187	GM10847	blood:	n/a	n/a
42	POLR2A	chr5:94889417-94891124	K562	blood:	n/a	n/a
43	TEAD4	chr5:94890490-94891056	HepG2	liver:	n/a	n/a
44	MAX	chr5:94890114-94891513	NB4	blood:	n/a	n/a
45	E2F6	chr5:94890595-94891243	K562	blood:	n/a	chr5:94890686-94890695 chr5:94890692-94890699 chr5:94890799-94890808 chr5:94890779-94890790
46	POLR2A	chr5:94890472-94891060	GM12891	blood:	n/a	n/a
47	POLR2A	chr5:94890280-94891261	Gliobla	brain:	n/a	n/a
48	POLR2A	chr5:94890307-94891163	MCF-7	breast:	n/a	n/a
49	MYC	chr5:94890053-94891264	K562	blood:	n/a	n/a
50	POLR2A	chr5:94890157-94891305	GM15510	blood:	n/a	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	chr5:94890265..94891768-chr5:95158248..95160600,2	K562	blood:
6	chr5:94885448..94888187-chr5:94888844..94890737,5	K562	blood:
7	chr5:94889331..94891668-chr5:96036859..96038572,2	K562	blood:

Variant related genes	Relation type
TTC37	TF binding region
ARSK	TF binding region
ENSG00000175449	Chromatin interaction
ENSG00000198677	Chromatin interaction
ENSG00000153113	Chromatin interaction
ENSG00000178015	Chromatin interaction
ENSG00000173221	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10040106	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs1123965	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1162859	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13162779	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2059786	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545842	0.86[LWK][hapmap];1.00[YRI][hapmap]
rs2560256	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560275	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2560276	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2731816	0.86[LWK][hapmap];0.92[YRI][hapmap]
rs2731818	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2731828	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4573018	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6556871	0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6556872	0.80[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2560277	TTC37	cis	Whole Blood	GTEx
rs2560277	TTC37	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94889000-94892200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr5:94889200-94892000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:94889200-94892000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:94889200-94892800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:94889400-94891400	Active TSS	Gastric	stomach
6	chr5:94889400-94891600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:94889400-94891600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr5:94889400-94891800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:94889400-94891800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:94889400-94891800	Active TSS	Stomach Mucosa	stomach
11	chr5:94889400-94891800	Active TSS	NHLF	lung
12	chr5:94889400-94892000	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr5:94889400-94892000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:94889400-94892000	Active TSS	Rectal Smooth Muscle	rectum
15	chr5:94889400-94892200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:94889600-94891400	Active TSS	Lung	lung
17	chr5:94889600-94891600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr5:94889600-94891600	Active TSS	HSMM	muscle
19	chr5:94889600-94891800	Active TSS	NHEK	skin
20	chr5:94889600-94892000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr5:94889600-94892000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:94889600-94892000	Active TSS	Right Atrium	heart
23	chr5:94889600-94892000	Active TSS	Right Ventricle	heart
24	chr5:94889600-94892000	Active TSS	K562	blood
25	chr5:94889600-94892200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:94889600-94892200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr5:94889600-94892400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr5:94889800-94891600	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr5:94889800-94891600	Active TSS	Fetal Kidney	kidney
30	chr5:94889800-94891600	Active TSS	Fetal Lung	lung
31	chr5:94889800-94891600	Active TSS	Placenta	Placenta
32	chr5:94889800-94891600	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr5:94889800-94891800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr5:94889800-94891800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:94889800-94891800	Active TSS	Colonic Mucosa	Colon
36	chr5:94889800-94891800	Active TSS	Fetal Intestine Small	intestine
37	chr5:94889800-94891800	Active TSS	Ovary	ovary
38	chr5:94889800-94891800	Active TSS	Pancreas	Pancrea
39	chr5:94889800-94891800	Active TSS	Placenta Amnion	Placenta Amnion
40	chr5:94889800-94892000	Active TSS	Fetal Intestine Large	intestine
41	chr5:94889800-94892000	Active TSS	A549	lung
42	chr5:94889800-94892000	Active TSS	GM12878-XiMat	blood
43	chr5:94889800-94892000	Active TSS	HMEC	breast
44	chr5:94889800-94892200	Active TSS	H1 Cell Line	embryonic stem cell
45	chr5:94889800-94892200	Active TSS	H9 Cell Line	embryonic stem cell
46	chr5:94889800-94892200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr5:94889800-94892200	Active TSS	Psoas Muscle	Psoas
48	chr5:94889800-94892200	Active TSS	HSMMtube	muscle
49	chr5:94889800-94892200	Active TSS	NHDF-Ad	bronchial
50	chr5:94890000-94891400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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