Variant report

Variant	rs1194593
Chromosome Location	chr1:154245512-154245513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:112)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:112 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154243503-154245611	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr1:154244415-154245873	SK-N-SH	brain:	n/a	chr1:154244811-154244823 chr1:154244813-154244823 chr1:154244812-154244825 chr1:154244809-154244828
3	SMC3	chr1:154244502-154245568	Hela-S3	cervix:	n/a	chr1:154244813-154244827
4	NRF1	chr1:154244475-154245673	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr1:154243903-154245572	Hela-S3	cervix:	n/a	n/a
6	CREB1	chr1:154244572-154245625	HepG2	liver:	n/a	n/a
7	YY1	chr1:154244623-154245723	GM12878	blood:	n/a	chr1:154244804-154244815 chr1:154244748-154244759
8	POLR2A	chr1:154243763-154245841	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:154244551-154245528	GM12878	blood:	n/a	n/a
10	JUND	chr1:154244571-154245592	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAFK	chr1:154244750-154245517	K562	blood:	n/a	n/a
12	CEBPB	chr1:154245334-154245550	K562	blood:	n/a	chr1:154245461-154245472
13	POLR2A	chr1:154244632-154245600	K562	blood:	n/a	n/a
14	PML	chr1:154244372-154245595	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:154244507-154245709	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:154244511-154245545	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:154244542-154245534	IMR90	lung:	n/a	n/a
18	NFIC	chr1:154244462-154245640	GM12878	blood:	n/a	n/a
19	ZNF384	chr1:154245414-154245827	GM12878	blood:	n/a	n/a
20	GATA3	chr1:154244458-154245563	A549	lung:	n/a	chr1:154244989-154244999
21	HCFC1	chr1:154243469-154245774	Hela-S3	cervix:	n/a	n/a
22	MXI1	chr1:154244597-154245555	Hela-S3	cervix:	n/a	n/a
23	BRCA1	chr1:154245496-154245576	Hela-S3	cervix:	n/a	n/a
24	FOS	chr1:154245440-154245621	MCF10A-Er-Src	breast:	n/a	n/a
25	JUND	chr1:154244650-154245632	K562	blood:	n/a	n/a
26	MYC	chr1:154244566-154245537	NB4	blood:	n/a	n/a
27	POLR2A	chr1:154244303-154245585	PANC-1	pancreas:	n/a	n/a
28	JUND	chr1:154245296-154245638	HepG2	liver:	n/a	n/a
29	ATF3	chr1:154244651-154245584	H1-hESC	embryonic stem cell:	n/a	n/a
30	EGR1	chr1:154244428-154245671	HCT-116	colon:	n/a	chr1:154244944-154244955 chr1:154244942-154244957
31	POLR2A	chr1:154243253-154245739	PFSK-1	brain:	n/a	n/a
32	POLR2A	chr1:154243737-154245602	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:154243911-154245675	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:154244590-154245566	GM19193	blood:	n/a	n/a
35	GTF3C2	chr1:154244883-154245673	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:154244599-154245735	K562	blood:	n/a	n/a
37	CEBPB	chr1:154245283-154245646	HepG2	liver:	n/a	chr1:154245461-154245472
38	YY1	chr1:154245305-154245871	GM12892	blood:	n/a	n/a
39	TAF1	chr1:154244499-154245576	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr1:154244576-154245557	K562	blood:	n/a	n/a
41	SIN3A	chr1:154244590-154245629	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr1:154244586-154245524	GM12891	blood:	n/a	n/a
43	POLR2A	chr1:154244569-154245630	HL-60	blood:	n/a	n/a
44	PML	chr1:154244514-154245525	K562	blood:	n/a	n/a
45	POLR2A	chr1:154244555-154245599	HCT-116	colon:	n/a	n/a
46	POLR2A	chr1:154244660-154245586	HEK293	kidney:	n/a	n/a
47	RAD21	chr1:154244415-154245624	HCT-116	colon:	n/a	chr1:154244811-154244823 chr1:154244813-154244823 chr1:154244812-154244825 chr1:154244809-154244828
48	ELK1	chr1:154245360-154245516	K562	blood:	n/a	n/a
49	CTCF	chr1:154244448-154245728	SK-N-SH	brain:	n/a	chr1:154244813-154244826 chr1:154244811-154244829 chr1:154244806-154244827
50	MAFK	chr1:154244565-154245577	Hela-S3	cervix:	n/a	n/a

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154244115..154246363-chr1:154579238..154580739,2	MCF-7	breast:
2	chr1:154154597..154158912-chr1:154243474..154246502,4	K562	blood:
3	chr1:154226522..154228397-chr1:154244257..154246291,2	MCF-7	breast:
4	chr1:154244396..154246200-chr1:154300299..154302808,2	MCF-7	breast:
5	chr1:153962369..153964805-chr1:154243433..154246826,4	MCF-7	breast:
6	chr1:154191724..154193429-chr1:154244687..154246204,2	MCF-7	breast:
7	chr1:154150174..154152704-chr1:154242243..154245750,3	MCF-7	breast:
8	chr1:154191842..154194909-chr1:154241050..154247826,7	K562	blood:
9	chr1:154191445..154194835-chr1:154242300..154245672,3	MCF-7	breast:
10	chr1:154162391..154165167-chr1:154243401..154246301,3	K562	blood:
11	chr1:154245017..154247132-chr20:55840387..55841981,2	MCF-7	breast:
12	chr1:154243817..154246754-chr1:154291993..154294660,2	K562	blood:
13	chr1:154244884..154247394-chr1:154296390..154298976,2	K562	blood:
14	chr1:154161792..154164519-chr1:154243896..154245592,2	MCF-7	breast:
15	chr1:154155037..154157341-chr1:154243497..154245632,3	MCF-7	breast:
16	chr1:153963157..153965644-chr1:154243334..154246314,2	K562	blood:
17	chr1:154153295..154155841-chr1:154244913..154246544,2	MCF-7	breast:
18	chr1:154236442..154241812-chr1:154243586..154247600,7	MCF-7	breast:

No data

Variant related genes	Relation type
HAX1	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143515	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000252817	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000143595	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10158820	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1044013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797047	0.88[ASN][1000 genomes]
rs11265238	0.91[JPT][hapmap]
rs11265251	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11265425	0.95[JPT][hapmap]
rs11586902	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11802893	0.82[JPT][hapmap]
rs1194596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023901	0.83[ASN][1000 genomes]
rs12025237	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12026177	0.91[JPT][hapmap]
rs12026615	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12027999	0.84[ASN][1000 genomes]
rs12028554	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12028949	0.91[JPT][hapmap]
rs12029331	0.86[ASN][1000 genomes]
rs12062977	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1212352	0.82[EUR][1000 genomes]
rs12733060	0.84[ASN][1000 genomes]
rs12738393	0.84[ASN][1000 genomes]
rs12743874	0.80[ASN][1000 genomes]
rs12750321	0.80[ASN][1000 genomes]
rs16835846	0.86[JPT][hapmap]
rs1760802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1760803	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1986709	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274993	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2282227	0.87[ASN][1000 genomes]
rs2340473	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2879788	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3762339	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3762340	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs3790613	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3790614	0.84[ASN][1000 genomes]
rs3811453	0.95[JPT][hapmap]
rs3811455	0.91[JPT][hapmap]
rs3828077	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs3935419	0.91[JPT][hapmap]
rs4240871	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4620534	0.91[JPT][hapmap]
rs6427509	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6657214	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6667222	0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs6673752	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6719	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7517578	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7524346	0.83[ASN][1000 genomes]
rs9803857	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9943093	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1194593	HAX1	cis	multi-tissue	Pritchard
rs1194593	UBAP2L	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154244000-154246000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:154244200-154245600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:154244200-154245600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:154244200-154245600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:154244200-154245600	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:154244200-154245600	Active TSS	Hela-S3	cervix
7	chr1:154244200-154245800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:154244200-154245800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:154244200-154245800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:154244200-154245800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:154244200-154245800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:154244200-154245800	Active TSS	Fetal Brain Female	brain
13	chr1:154244200-154246000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr1:154244200-154246200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:154244200-154246200	Active TSS	A549	lung
16	chr1:154244200-154246400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:154244400-154245600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:154244400-154245600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr1:154244400-154245600	Active TSS	Brain Hippocampus Middle	brain
20	chr1:154244400-154245600	Active TSS	Fetal Intestine Large	intestine
21	chr1:154244400-154245600	Active TSS	Fetal Lung	lung
22	chr1:154244400-154245600	Active TSS	Rectal Smooth Muscle	rectum
23	chr1:154244400-154245600	Active TSS	NH-A	brain
24	chr1:154244400-154245800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:154244400-154245800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:154244400-154245800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:154244400-154245800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:154244400-154245800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:154244400-154245800	Active TSS	Aorta	Aorta
30	chr1:154244400-154245800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:154244400-154245800	Active TSS	Ovary	ovary
32	chr1:154244400-154245800	Active TSS	Right Ventricle	heart
33	chr1:154244400-154245800	Active TSS	Thymus	Thymus
34	chr1:154244400-154245800	Active TSS	GM12878-XiMat	blood
35	chr1:154244400-154245800	Active TSS	K562	blood
36	chr1:154244400-154246000	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:154244400-154246000	Active TSS	H9 Cell Line	embryonic stem cell
38	chr1:154244400-154246000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:154244400-154246000	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr1:154244400-154246000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:154244400-154246000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:154244400-154246000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:154244400-154246000	Active TSS	Fetal Kidney	kidney
44	chr1:154244400-154246000	Active TSS	Right Atrium	heart
45	chr1:154244400-154246000	Active TSS	NHDF-Ad	bronchial
46	chr1:154244400-154246200	Active TSS	HSMMtube	muscle
47	chr1:154244400-154246400	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr1:154244600-154245600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:154244600-154245600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:154244600-154245600	Active TSS	Primary T killer memory cells from peripheral blood	blood

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