Variant report

Variant	rs3754359
Chromosome Location	chr1:228272155-228272156
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	POLR2A	chr1:228269815-228272522	GM12892	blood:	n/a	n/a
2	RCOR1	chr1:228271963-228272381	K562	blood:	n/a	n/a
3	FOS	chr1:228271992-228272473	MCF10A-Er-Src	breast:	n/a	chr1:228272202-228272210 chr1:228272200-228272211 chr1:228272200-228272212 chr1:228272025-228272039
4	MXI1	chr1:228269786-228272826	IMR90	lung:	n/a	chr1:228269970-228269979
5	CEBPB	chr1:228271668-228272530	K562	blood:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
6	CEBPB	chr1:228272084-228272544	HepG2	liver:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
7	POLR2A	chr1:228268843-228274035	GM12878	blood:	n/a	n/a
8	MYC	chr1:228271688-228272626	MCF10A-Er-Src	breast:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
9	MAX	chr1:228271537-228272602	NB4	blood:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
10	CEBPB	chr1:228271667-228272505	IMR90	lung:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
11	POLR2A	chr1:228271358-228272331	GM12891	blood:	n/a	n/a
12	MAX	chr1:228271707-228272413	GM12878	blood:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
13	POLR2A	chr1:228272137-228272343	GM12878	blood:	n/a	n/a
14	CEBPB	chr1:228272018-228272495	MCF-7	breast:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
15	POLR2A	chr1:228268861-228272292	K562	blood:	n/a	n/a
16	MYC	chr1:228269434-228272362	K562	blood:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
17	SIN3AK20	chr1:228269812-228272410	K562	blood:	n/a	n/a
18	TBL1XR1	chr1:228271690-228273696	K562	blood:	n/a	n/a
19	CEBPB	chr1:228272114-228272489	A549	lung:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
20	MYC	chr1:228268849-228272477	K562	blood:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269015-228269031 chr1:228269970-228269980 chr1:228269972-228269979 chr1:228269039-228269048
21	RCOR1	chr1:228271926-228272407	K562	blood:	n/a	n/a
22	POLR2A	chr1:228269801-228272179	HUVEC	blood vessel:	n/a	n/a
23	CEBPB	chr1:228272119-228272497	HepG2	liver:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
24	CEBPB	chr1:228272040-228272574	A549	lung:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
25	MAFF	chr1:228272029-228272326	K562	blood:	n/a	n/a
26	E2F4	chr1:228272108-228272300	MCF10A-Er-Src	breast:	n/a	chr1:228272173-228272182
27	MXI1	chr1:228268732-228272801	SK-N-SH	brain:	n/a	chr1:228269970-228269979
28	HDAC2	chr1:228271896-228272364	K562	blood:	n/a	n/a
29	POLR2A	chr1:228271948-228272169	ProgFib	skin:	n/a	n/a
30	MAFK	chr1:228271487-228272383	IMR90	lung:	n/a	chr1:228271709-228271723 chr1:228271706-228271721 chr1:228271711-228271722 chr1:228271710-228271721 chr1:228271710-228271721 chr1:228271706-228271722 chr1:228271711-228271722
31	STAT3	chr1:228272143-228272343	MCF10A-Er-Src	breast:	n/a	n/a
32	MXI1	chr1:228271328-228272199	K562	blood:	n/a	n/a
33	CEBPB	chr1:228271750-228272487	HepG2	liver:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272300-228272311
34	MAX	chr1:228269245-228272380	HepG2	liver:	n/a	chr1:228271848-228271859 chr1:228269763-228269773 chr1:228269970-228269981 chr1:228271849-228271856 chr1:228270033-228270043 chr1:228269970-228269980 chr1:228269972-228269979
35	WRNIP1	chr1:228270941-228273725	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:228270855-228272420	GM12892	blood:	n/a	n/a
37	NFATC1	chr1:228271808-228272799	GM12878	blood:	n/a	n/a
38	FOS	chr1:228272059-228272363	MCF10A-Er-Src	breast:	n/a	chr1:228272202-228272210 chr1:228272200-228272211 chr1:228272200-228272212
39	MAX	chr1:228271676-228272232	HepG2	liver:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
40	ZNF263	chr1:228271063-228272260	HEK293-T-REx	kidney:	n/a	n/a
41	CHD1	chr1:228269799-228274173	IMR90	lung:	n/a	n/a
42	CEBPB	chr1:228272110-228272465	K562	blood:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272300-228272311
43	POLR2A	chr1:228271444-228273196	U87	brain:	n/a	n/a
44	POLR2A	chr1:228269015-228272289	GM18505	blood:	n/a	n/a
45	POLR2A	chr1:228272015-228272323	GM12878	blood:	n/a	n/a
46	FOS	chr1:228271926-228272535	HUVEC	blood vessel:	n/a	chr1:228272202-228272210 chr1:228272200-228272211 chr1:228272200-228272212 chr1:228272025-228272039
47	BATF	chr1:228272033-228272345	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:228271945-228272377	MCF-7	breast:	n/a	n/a
49	POLR2A	chr1:228272124-228272646	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:228269884-228272412	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
2	chr1:227921488..227923041-chr1:228269667..228272192,2	MCF-7	breast:
3	chr1:228192379..228197446-chr1:228268248..228273367,9	MCF-7	breast:
4	chr1:228271061..228272928-chr1:228645504..228647273,2	K562	blood:
5	chr1:227916348..227918529-chr1:228270679..228272482,2	MCF-7	breast:
6	chr1:228271974..228275319-chr1:228643789..228645457,3	K562	blood:
7	chr1:228269773..228272364-chr1:228352112..228354622,6	MCF-7	breast:
8	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
9	chr1:228244560..228247525-chr1:228272017..228274884,2	MCF-7	breast:
10	chr1:228271007..228273553-chr1:228330538..228333178,2	MCF-7	breast:
11	chr1:228271816..228272376-chr1:228290019..228290721,2	K562	blood:
12	chr1:228187607..228189988-chr1:228271798..228274148,2	K562	blood:
13	chr1:228272139..228273835-chr1:228675045..228676865,2	MCF-7	breast:
14	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
15	chr1:228270141..228272243-chr1:228325927..228327960,2	MCF-7	breast:
16	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
17	chr1:228270694..228272754-chr8:126441550..126443960,2	MCF-7	breast:
18	chr1:228270474..228272694-chr1:228336357..228338344,2	K562	blood:
19	chr1:227973508..227976414-chr1:228271906..228274660,2	K562	blood:

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000196890	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000154342	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000143793	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12026579	0.92[AMR][1000 genomes]
rs12031390	0.92[AMR][1000 genomes]
rs12038612	0.92[AMR][1000 genomes]
rs12039528	0.92[AMR][1000 genomes]
rs12040506	0.92[AMR][1000 genomes]
rs12044962	0.92[AMR][1000 genomes]
rs12049152	0.92[AMR][1000 genomes]
rs2298013	0.92[AMR][1000 genomes]
rs3754358	1.00[ASW][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes]
rs55686465	0.92[AFR][1000 genomes]
rs56003736	0.92[AFR][1000 genomes]
rs56029925	0.92[AFR][1000 genomes]
rs56080014	0.85[AFR][1000 genomes]
rs56154605	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58045861	0.85[AFR][1000 genomes]
rs61230585	0.92[AFR][1000 genomes]
rs74140905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140910	0.92[AFR][1000 genomes]
rs74140916	0.92[AFR][1000 genomes]
rs74140919	0.92[AFR][1000 genomes]
rs74140923	0.92[AFR][1000 genomes]
rs74140953	0.92[AFR][1000 genomes]
rs74140954	0.92[AFR][1000 genomes]
rs74140955	0.92[AFR][1000 genomes]
rs74140956	0.92[AFR][1000 genomes]
rs74140957	0.92[AFR][1000 genomes]
rs74140962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140963	0.92[AFR][1000 genomes]
rs74140967	0.92[AFR][1000 genomes]
rs74140968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74140971	0.85[AFR][1000 genomes]
rs74140972	0.85[AFR][1000 genomes]
rs74140973	0.85[AFR][1000 genomes]
rs74140974	0.85[AFR][1000 genomes]
rs74140975	0.85[AFR][1000 genomes]
rs74140976	0.85[AFR][1000 genomes]
rs74140977	0.85[AFR][1000 genomes]
rs74140978	0.85[AFR][1000 genomes]
rs74140980	0.85[AFR][1000 genomes]
rs74140981	0.85[AFR][1000 genomes]
rs74140982	0.85[AFR][1000 genomes]
rs74140985	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74143629	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74143633	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
12	esv3395884	chr1:228269354-228272202	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 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	chr1:228269000-228272200	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:228269200-228272200	Active TSS	Right Atrium	heart
3	chr1:228269200-228272400	Active TSS	NHLF	lung
4	chr1:228269400-228272400	Active TSS	HSMM	muscle
5	chr1:228269400-228272600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:228269600-228272200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:228269600-228272200	Active TSS	Gastric	stomach
8	chr1:228269600-228272200	Active TSS	Ovary	ovary
9	chr1:228269600-228272200	Active TSS	Small Intestine	intestine
10	chr1:228269600-228272400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:228269600-228272400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:228269600-228272400	Active TSS	Aorta	Aorta
13	chr1:228269600-228272400	Active TSS	HSMMtube	muscle
14	chr1:228269600-228272400	Active TSS	NHDF-Ad	bronchial
15	chr1:228269600-228272600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:228269600-228272600	Active TSS	Lung	lung
17	chr1:228269600-228272600	Active TSS	Psoas Muscle	Psoas
18	chr1:228270200-228272400	Active TSS	Fetal Muscle Trunk	muscle
19	chr1:228270800-228272200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:228271000-228272200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:228271000-228272200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr1:228271000-228272800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr1:228271000-228273000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:228271000-228273400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:228271000-228273600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr1:228271000-228273600	Transcr. at gene 5' and 3'	Dnd41	blood
27	chr1:228271000-228273800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr1:228271000-228274000	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:228271200-228272200	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr1:228271200-228272200	Transcr. at gene 5' and 3'	Thymus	Thymus
31	chr1:228271200-228272400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr1:228271200-228272400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr1:228271200-228272400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr1:228271200-228272600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr1:228271200-228272800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
36	chr1:228271200-228273200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:228271200-228273600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:228271200-228274000	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr1:228271400-228272200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:228271400-228272200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
41	chr1:228271400-228272200	Transcr. at gene 5' and 3'	Osteobl	bone
42	chr1:228271400-228272400	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr1:228271400-228272400	Flanking Active TSS	Fetal Brain Male	brain
44	chr1:228271400-228272400	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr1:228271400-228272400	Flanking Active TSS	Fetal Thymus	thymus
46	chr1:228271400-228272400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:228271400-228272800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr1:228271400-228272800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr1:228271400-228272800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:228271400-228272800	Flanking Active TSS	Fetal Brain Female	brain

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