Variant report

Variant	rs3754210
Chromosome Location	chr1:150954261-150954262
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	MYBL2	chr1:150954074-150955130	HepG2	liver:	n/a	n/a
2	PML	chr1:150953613-150955128	MCF-7	breast:	n/a	n/a
3	RXRA	chr1:150954220-150954801	HepG2	liver:	n/a	chr1:150954570-150954577
4	ZNF217	chr1:150953711-150954952	MCF-7	breast:	n/a	n/a
5	HA-E2F1	chr1:150953516-150954874	MCF-7	breast:	n/a	n/a
6	EP300	chr1:150953548-150954677	ECC-1	luminal epithelium:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
7	ESR1	chr1:150954059-150954941	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr1:150953807-150954405	H1-hESC	embryonic stem cell:	n/a	chr1:150954010-150954019
9	EP300	chr1:150953533-150954895	HepG2	liver:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
10	NR2F2	chr1:150953437-150955516	MCF-7	breast:	n/a	n/a
11	MAX	chr1:150953445-150955230	MCF-7	breast:	n/a	chr1:150954010-150954019
12	ZBTB7A	chr1:150954225-150954563	HepG2	liver:	n/a	n/a
13	SP1	chr1:150953551-150954550	H1-hESC	embryonic stem cell:	n/a	chr1:150953843-150953852 chr1:150953939-150953948 chr1:150953844-150953853 chr1:150953842-150953854 chr1:150953937-150953949 chr1:150953843-150953853 chr1:150953938-150953947 chr1:150953816-150953830 chr1:150953843-150953857 chr1:150953842-150953854 chr1:150953937-150953949 chr1:150953843-150953852 chr1:150953843-150953853
14	SIN3AK20	chr1:150953478-150955152	MCF-7	breast:	n/a	n/a
15	SIN3AK20	chr1:150953436-150955846	MCF-7	breast:	n/a	n/a
16	TEAD4	chr1:150953496-150954733	ECC-1	luminal epithelium:	n/a	n/a
17	NFIC	chr1:150954208-150954755	HepG2	liver:	n/a	n/a
18	EP300	chr1:150953472-150954827	HepG2	liver:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
19	HNF4G	chr1:150954234-150954853	HepG2	liver:	n/a	n/a
20	ESR1	chr1:150954238-150954636	T-47D	breast:	n/a	n/a
21	GATA3	chr1:150954133-150954620	T-47D	breast:	n/a	n/a
22	MAX	chr1:150953420-150955157	HepG2	liver:	n/a	chr1:150954010-150954019
23	ESR1	chr1:150954186-150954656	ECC-1	luminal epithelium:	n/a	n/a
24	ESR1	chr1:150954147-150954586	ECC-1	luminal epithelium:	n/a	n/a
25	JUN	chr1:150953849-150954281	H1-hESC	embryonic stem cell:	n/a	chr1:150953937-150953946
26	ESR1	chr1:150954027-150954921	ECC-1	luminal epithelium:	n/a	n/a
27	NFIC	chr1:150953644-150955029	ECC-1	luminal epithelium:	n/a	n/a
28	GATA3	chr1:150953803-150954956	MCF-7	breast:	n/a	n/a
29	POLR2A	chr1:150953342-150954973	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr1:150953545-150955004	HepG2	liver:	n/a	n/a
31	YY1	chr1:150954234-150954840	HepG2	liver:	n/a	n/a
32	EP300	chr1:150953590-150955177	ECC-1	luminal epithelium:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
33	TEAD4	chr1:150953538-150954765	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:150953545-150954447	MCF-7	breast:	n/a	n/a
35	CEBPB	chr1:150953482-150955441	MCF-7	breast:	n/a	chr1:150954007-150954018
36	POLR2A	chr1:150954214-150954371	HepG2	liver:	n/a	n/a
37	TEAD4	chr1:150954139-150954559	H1-hESC	embryonic stem cell:	n/a	n/a
38	ESR1	chr1:150954156-150954632	T-47D	breast:	n/a	n/a
39	GATA3	chr1:150953478-150955241	MCF-7	breast:	n/a	n/a
40	EP300	chr1:150953650-150955136	MCF-7	breast:	n/a	chr1:150953929-150953945 chr1:150953966-150953982
41	TCF12	chr1:150953466-150955066	MCF-7	breast:	n/a	chr1:150953966-150953976 chr1:150954259-150954266 chr1:150953905-150953912
42	MYBL2	chr1:150954166-150954812	HepG2	liver:	n/a	n/a
43	HNF4G	chr1:150954197-150954824	HepG2	liver:	n/a	n/a
44	GATA3	chr1:150954209-150954552	MCF-7	breast:	n/a	n/a
45	TEAD4	chr1:150953591-150955038	MCF-7	breast:	n/a	n/a
46	MAFK	chr1:150954098-150954865	HepG2	liver:	n/a	n/a
47	NFIC	chr1:150953447-150955016	ECC-1	luminal epithelium:	n/a	n/a
48	ESR1	chr1:150954172-150954579	ECC-1	luminal epithelium:	n/a	n/a
49	HNF4A	chr1:150954240-150954851	HepG2	liver:	n/a	n/a
50	USF1	chr1:150953681-150954938	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150238576..150241529-chr1:150952972..150954986,2	MCF-7	breast:
2	chr1:150951645..150956254-chr1:150963775..150970753,11	MCF-7	breast:
3	chr1:150951870..150954741-chr1:151030040..151032027,2	K562	blood:
4	chr1:150951620..150955085-chr1:150979651..150983018,4	K562	blood:
5	chr1:150943576..150944631-chr1:150954006..150954679,3	MCF-7	breast:
6	chr1:150953914..150954774-chr1:150980327..150981076,4	MCF-7	breast:
7	chr1:150533380..150535959-chr1:150953578..150956750,3	MCF-7	breast:
8	chr1:150952182..150958148-chr1:150976816..150982947,12	MCF-7	breast:
9	chr1:150954083..150955944-chr1:151254218..151255800,2	MCF-7	breast:
10	chr1:150549116..150552105-chr1:150952338..150954284,2	MCF-7	breast:
11	chr1:150950574..150954547-chr1:151027400..151032185,6	MCF-7	breast:
12	chr1:150539071..150540911-chr1:150952638..150955044,2	MCF-7	breast:
13	chr1:150953971..150955993-chr7:99715179..99717200,2	MCF-7	breast:
14	chr1:150952337..150955570-chr1:151040233..151043325,3	MCF-7	breast:
15	chr1:150952576..150954333-chr7:75931969..75934548,2	MCF-7	breast:
16	chr1:149856818..149859748-chr1:150952737..150955704,2	MCF-7	breast:

Variant related genes	Relation type
ANXA9	TF binding region
ENSG00000143363	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000117362	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000118292	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000106211	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000264508	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000143409	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11204727	0.92[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.94[TSI][hapmap]
rs11579289	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040707	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12042263	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12044969	0.98[ASN][1000 genomes]
rs16832604	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134688	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs2305812	0.93[CHB][hapmap];0.96[CHD][hapmap];0.92[ASN][1000 genomes]
rs2305815	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs267736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34090972	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738483	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs3820541	0.91[CEU][hapmap]
rs4379678	0.92[CEU][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs533928	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs539118	0.96[ASN][1000 genomes]
rs61817649	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6671489	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6679701	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs6688248	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72706512	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517566	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap]
rs7521445	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535032	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7535848	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs771203	0.96[ASN][1000 genomes]
rs771204	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs771205	0.93[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3754210	CTSK	cis	Artery Aorta	GTEx
rs3754210	ARNT	cis	Whole Blood	GTEx
rs3754210	ANXA9,FAM63A	cis	brain	BrainEAC
rs3754210	ARNT	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
2	chr1:150952200-150955000	Weak transcription	Brain Germinal Matrix	brain
3	chr1:150952400-150954400	Enhancers	Liver	Liver
4	chr1:150952600-150954400	Weak transcription	Fetal Lung	lung
5	chr1:150952600-150954800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:150952600-150957800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:150952600-150960800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:150952600-150968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:150953200-150955400	Enhancers	Placenta	Placenta
10	chr1:150953200-150955400	Enhancers	Fetal Thymus	thymus
11	chr1:150953200-150956200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:150953200-150956200	Enhancers	Fetal Intestine Large	intestine
13	chr1:150953200-150956200	Enhancers	HMEC	breast
14	chr1:150953400-150954600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:150953400-150954600	Flanking Active TSS	Hela-S3	cervix
16	chr1:150953400-150955000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:150953400-150955000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:150953400-150955400	Enhancers	H9 Cell Line	embryonic stem cell
19	chr1:150953400-150955400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:150953400-150955400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:150953600-150954400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:150953600-150954400	Enhancers	Pancreas	Pancrea
23	chr1:150953600-150954600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:150953600-150954800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:150953600-150954800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:150953600-150954800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:150953600-150954800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:150953600-150954800	Enhancers	Fetal Kidney	kidney
29	chr1:150953600-150954800	Enhancers	Thymus	Thymus
30	chr1:150953600-150954800	Enhancers	NHLF	lung
31	chr1:150953600-150955000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:150953600-150955000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:150953600-150955000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:150953600-150955000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:150953600-150955000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:150953600-150955000	Flanking Active TSS	A549	lung
37	chr1:150953600-150955000	Enhancers	Osteobl	bone
38	chr1:150953600-150955200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:150953600-150955200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:150953600-150955200	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr1:150953600-150955400	Enhancers	Stomach Mucosa	stomach
42	chr1:150953600-150955400	Enhancers	K562	blood
43	chr1:150953600-150955800	Enhancers	Fetal Intestine Small	intestine
44	chr1:150953600-150955800	Flanking Active TSS	HepG2	liver
45	chr1:150953600-150959000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:150953800-150954400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:150953800-150954400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:150953800-150954400	Flanking Active TSS	NHEK	skin
49	chr1:150953800-150954600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:150953800-150954600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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