Variant report

Variant	rs2735593
Chromosome Location	chr1:85742338-85742339
allele	C/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	BACH1	chr1:85742088-85742652	H1-hESC	embryonic stem cell:	n/a	n/a
2	BRCA1	chr1:85742196-85742409	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:85741401-85742816	HepG2	liver:	n/a	n/a
4	EP300	chr1:85742028-85742782	GM12878	blood:	n/a	chr1:85742765-85742779 chr1:85742651-85742660
5	SRF	chr1:85741461-85743025	HCT-116	colon:	n/a	n/a
6	POLR2A	chr1:85741574-85742850	ProgFib	skin:	n/a	n/a
7	TAF1	chr1:85741634-85742811	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr1:85741693-85742708	HepG2	liver:	n/a	n/a
9	GTF2F1	chr1:85741736-85742791	Hela-S3	cervix:	n/a	n/a
10	CREB1	chr1:85741866-85742881	ECC-1	luminal epithelium:	n/a	n/a
11	GABPA	chr1:85741710-85742733	A549	lung:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
12	STAT1	chr1:85741632-85742729	GM12878	blood:	n/a	n/a
13	RAD21	chr1:85741588-85742394	IMR90	lung:	n/a	chr1:85742287-85742296
14	ZMIZ1	chr1:85741796-85742815	K562	blood:	n/a	n/a
15	MAX	chr1:85741883-85742702	HepG2	liver:	n/a	chr1:85741944-85741954
16	SP1	chr1:85741954-85742690	K562	blood:	n/a	chr1:85742217-85742229 chr1:85742135-85742149 chr1:85742400-85742411 chr1:85742138-85742150 chr1:85742522-85742532 chr1:85742218-85742227 chr1:85742087-85742099 chr1:85742087-85742099 chr1:85742088-85742097 chr1:85742217-85742229
17	E2F6	chr1:85742147-85742571	K562	blood:	n/a	chr1:85742283-85742294
18	POLR2A	chr1:85741719-85742814	K562	blood:	n/a	n/a
19	GABPA	chr1:85741658-85742949	SK-N-SH	brain:	n/a	chr1:85741945-85741954 chr1:85741911-85741918
20	POLR2A	chr1:85741694-85742784	Hela-S3	cervix:	n/a	n/a
21	NRF1	chr1:85742277-85742672	Hela-S3	cervix:	n/a	chr1:85742461-85742472
22	POLR2A	chr1:85740468-85743570	PANC-1	pancreas:	n/a	n/a
23	EBF1	chr1:85742052-85742879	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:85740591-85742964	GM12891	blood:	n/a	n/a
25	YY1	chr1:85741871-85742595	GM12892	blood:	n/a	chr1:85742079-85742093 chr1:85741942-85741951 chr1:85742166-85742180
26	RFX5	chr1:85742145-85742791	GM12878	blood:	n/a	n/a
27	ZNF143	chr1:85741679-85742630	H1-hESC	embryonic stem cell:	n/a	chr1:85741944-85741954
28	SRF	chr1:85741870-85742978	MCF-7	breast:	n/a	n/a
29	POLR2A	chr1:85741655-85742724	K562	blood:	n/a	n/a
30	ELF1	chr1:85741703-85742743	K562	blood:	n/a	chr1:85742651-85742662 chr1:85742210-85742219 chr1:85742209-85742222 chr1:85742343-85742355
31	ELF1	chr1:85741515-85742975	HCT-116	colon:	n/a	chr1:85742651-85742662 chr1:85742210-85742219 chr1:85742209-85742222 chr1:85742343-85742355
32	POLR2A	chr1:85741835-85742839	HepG2	liver:	n/a	n/a
33	MXI1	chr1:85742287-85742789	H1-hESC	embryonic stem cell:	n/a	n/a
34	CREB1	chr1:85741830-85742702	A549	lung:	n/a	n/a
35	TAF1	chr1:85741434-85742652	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr1:85741665-85742849	NB4	blood:	n/a	chr1:85741944-85741954
37	KAP1	chr1:85740518-85742974	HEK293	kidney:	n/a	chr1:85741050-85741059
38	RELA	chr1:85740582-85742917	GM12878	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
39	POLR2A	chr1:85741210-85742785	GM12878	blood:	n/a	n/a
40	NFYB	chr1:85742123-85742570	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:85741369-85742939	Raji	blood:	n/a	n/a
42	POLR2A	chr1:85741820-85742814	HEK293	kidney:	n/a	n/a
43	EGR1	chr1:85742296-85742586	GM12878	blood:	n/a	chr1:85742430-85742444
44	MTA3	chr1:85741236-85742914	GM12878	blood:	n/a	n/a
45	SIN3AK20	chr1:85741893-85742344	HepG2	liver:	n/a	n/a
46	TCF3	chr1:85741866-85742633	GM12878	blood:	n/a	chr1:85741958-85741972
47	HEY1	chr1:85741619-85742871	HepG2	liver:	n/a	chr1:85741928-85741943 chr1:85742088-85742103 chr1:85742080-85742095
48	MYC	chr1:85741486-85742880	NB4	blood:	n/a	chr1:85741944-85741954
49	ELK4	chr1:85741271-85742801	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr1:85740603-85742874	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
2	chr1:85742187..85745018-chr1:85749555..85753087,3	K562	blood:
3	chr1:85742188..85743029-chr1:149223809..149224656,2	Hela-S3	cervix:
4	chr1:85665913..85668656-chr1:85741362..85743092,3	MCF-7	breast:
5	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
6	chr1:85741753..85742600-chr17:48133754..48134482,2	Hela-S3	cervix:
7	chr1:85741939..85742635-chr3:156391987..156392721,2	Hela-S3	cervix:
8	chr1:85740856..85742558-chr1:86046586..86048600,2	MCF-7	breast:
9	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
10	chr1:85741740..85742671-chr16:577325..578168,2	Hela-S3	cervix:
11	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
12	chr1:85665227..85667257-chr1:85740935..85743875,2	K562	blood:
13	chr1:85741905..85744580-chr1:85747619..85751624,6	K562	blood:
14	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYR61-3	chr1:85742041-85742480	NONHSAT004241

Variant related genes	Relation type
ENSG00000223653	TF binding region
ENSG00000264380	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000005884	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000162642	Chromatin interaction
ENSG00000103326	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493762	0.82[JPT][hapmap]
rs11161556	0.91[EUR][1000 genomes]
rs11161574	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11161584	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11577656	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11583836	0.83[CEU][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes]
rs12563295	0.88[EUR][1000 genomes]
rs17123650	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2252408	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs233101	0.83[CHB][hapmap]
rs2647396	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2735587	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2735588	0.88[ASN][1000 genomes]
rs2735591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2735592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2735594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36006436	0.88[EUR][1000 genomes]
rs4907139	0.83[JPT][hapmap]
rs4949892	0.93[EUR][1000 genomes]
rs4949926	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60156243	0.93[EUR][1000 genomes]
rs6663690	0.83[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs6671589	0.81[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6693365	0.94[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72722624	0.87[EUR][1000 genomes]
rs72722631	0.88[EUR][1000 genomes]
rs72722638	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72722643	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2735593	C1orf52	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85739200-85743000	Active TSS	Psoas Muscle	Psoas
2	chr1:85739800-85742800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:85740200-85743200	Active TSS	Colonic Mucosa	Colon
4	chr1:85740400-85742400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:85740400-85742600	Active TSS	GM12878-XiMat	blood
6	chr1:85740400-85742800	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr1:85740600-85742800	Active TSS	Fetal Intestine Large	intestine
8	chr1:85740600-85742800	Active TSS	Ovary	ovary
9	chr1:85740600-85743000	Active TSS	Right Atrium	heart
10	chr1:85740600-85743000	Active TSS	Right Ventricle	heart
11	chr1:85740600-85743200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:85740600-85743200	Active TSS	Esophagus	oesophagus
13	chr1:85740800-85742600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:85740800-85742600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr1:85740800-85742600	Active TSS	HMEC	breast
16	chr1:85740800-85742600	Active TSS	NHEK	skin
17	chr1:85740800-85742800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:85740800-85742800	Active TSS	Left Ventricle	heart
19	chr1:85740800-85742800	Active TSS	Stomach Mucosa	stomach
20	chr1:85740800-85742800	Active TSS	NHDF-Ad	bronchial
21	chr1:85740800-85742800	Active TSS	NHLF	lung
22	chr1:85740800-85743000	Active TSS	Aorta	Aorta
23	chr1:85740800-85743400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:85741000-85742600	Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:85741000-85742600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr1:85741000-85742600	Active TSS	NH-A	brain
27	chr1:85741000-85742800	Active TSS	HSMM	muscle
28	chr1:85741000-85742800	Active TSS	HUVEC	blood vessel
29	chr1:85741000-85743000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:85741000-85743000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:85741000-85743000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:85741000-85743000	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:85741000-85743000	Active TSS	Fetal Muscle Leg	muscle
34	chr1:85741000-85743200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr1:85741000-85743200	Active TSS	H9 Cell Line	embryonic stem cell
36	chr1:85741000-85743200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:85741200-85742600	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:85741200-85742600	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:85741200-85742600	Active TSS	Osteobl	bone
40	chr1:85741200-85742800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:85741200-85742800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:85741200-85742800	Active TSS	Fetal Intestine Small	intestine
43	chr1:85741200-85742800	Active TSS	Small Intestine	intestine
44	chr1:85741200-85742800	Active TSS	K562	blood
45	chr1:85741200-85743000	Active TSS	H1 Cell Line	embryonic stem cell
46	chr1:85741200-85743000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:85741200-85743000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:85741200-85743000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:85741200-85743000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:85741200-85743000	Active TSS	Colon Smooth Muscle	Colon

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