Variant report

Variant	rs3754358
Chromosome Location	chr1:228271909-228271910
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	MXI1	chr1:228269786-228272826	IMR90	lung:	n/a	chr1:228269970-228269979
3	CEBPB	chr1:228271668-228272530	K562	blood:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
4	YY1	chr1:228271597-228272021	K562	blood:	n/a	n/a
5	CREB1	chr1:228269350-228271910	HepG2	liver:	n/a	chr1:228270390-228270403
6	MAX	chr1:228271682-228272099	H1-hESC	embryonic stem cell:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
7	POLR2A	chr1:228268843-228274035	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:228269867-228272065	HUVEC	blood vessel:	n/a	n/a
9	MYC	chr1:228271688-228272626	MCF10A-Er-Src	breast:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
10	MAX	chr1:228271537-228272602	NB4	blood:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
11	POLR2A	chr1:228269831-228272124	PFSK-1	brain:	n/a	n/a
12	CEBPB	chr1:228271667-228272505	IMR90	lung:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272477-228272488 chr1:228272300-228272311
13	MAX	chr1:228271423-228271967	Hela-S3	cervix:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
14	POLR2A	chr1:228271358-228272331	GM12891	blood:	n/a	n/a
15	MAX	chr1:228271707-228272413	GM12878	blood:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
16	POLR2A	chr1:228269191-228271920	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:228268861-228272292	K562	blood:	n/a	n/a
18	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
19	POLR2A	chr1:228271632-228272111	PANC-1	pancreas:	n/a	n/a
20	SIN3AK20	chr1:228269812-228272410	K562	blood:	n/a	n/a
21	TBL1XR1	chr1:228271690-228273696	K562	blood:	n/a	n/a
22	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
23	POLR2A	chr1:228269241-228272029	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:228269801-228272179	HUVEC	blood vessel:	n/a	n/a
25	UBTF	chr1:228269404-228271957	K562	blood:	n/a	n/a
26	MXI1	chr1:228268732-228272801	SK-N-SH	brain:	n/a	chr1:228269970-228269979
27	HDAC2	chr1:228271896-228272364	K562	blood:	n/a	n/a
28	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
29	POLR2A	chr1:228270010-228271936	H1-hESC	embryonic stem cell:	n/a	n/a
30	MXI1	chr1:228271328-228272199	K562	blood:	n/a	n/a
31	CEBPB	chr1:228271750-228272487	HepG2	liver:	n/a	chr1:228272300-228272313 chr1:228272302-228272313 chr1:228272300-228272311
32	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
33	MAX	chr1:228270859-228272047	ECC-1	luminal epithelium:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
34	WRNIP1	chr1:228270941-228273725	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:228270855-228272420	GM12892	blood:	n/a	n/a
36	NFATC1	chr1:228271808-228272799	GM12878	blood:	n/a	n/a
37	MAX	chr1:228271676-228272232	HepG2	liver:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
38	ZNF263	chr1:228271063-228272260	HEK293-T-REx	kidney:	n/a	n/a
39	POLR2A	chr1:228271602-228271928	GM12878	blood:	n/a	n/a
40	CHD1	chr1:228269799-228274173	IMR90	lung:	n/a	n/a
41	CTCF	chr1:228271780-228271930	RPTEC	kidney:	n/a	n/a
42	POLR2A	chr1:228268831-228271953	K562	blood:	n/a	n/a
43	POLR2A	chr1:228271444-228273196	U87	brain:	n/a	n/a
44	POLR2A	chr1:228269015-228272289	GM18505	blood:	n/a	n/a
45	SMC3	chr1:228271665-228271953	HepG2	liver:	n/a	n/a
46	POLR2A	chr1:228269884-228272412	MCF10A-Er-Src	breast:	n/a	n/a
47	MYC	chr1:228271688-228271953	HUVEC	blood vessel:	n/a	chr1:228271848-228271859 chr1:228271849-228271856
48	MAZ	chr1:228268871-228272552	IMR90	lung:	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
49	MAZ	chr1:228269209-228272123	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
50	BACH1	chr1:228271612-228272587	K562	blood:	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	chr1:228269794..228271921-chr1:228327972..228330804,3	MCF-7	breast:
6	chr1:227916348..227918529-chr1:228270679..228272482,2	MCF-7	breast:
7	chr1:228271073..228272063-chr1:228289733..228290720,3	MCF-7	breast:
8	chr1:228269773..228272364-chr1:228352112..228354622,6	MCF-7	breast:
9	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
10	chr1:228271007..228273553-chr1:228330538..228333178,2	MCF-7	breast:
11	chr1:228270338..228271968-chr1:228400103..228402238,2	MCF-7	breast:
12	chr1:228271816..228272376-chr1:228290019..228290721,2	K562	blood:
13	chr1:228187607..228189988-chr1:228271798..228274148,2	K562	blood:
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	chr1:228270437..228272083-chr1:228644163..228645827,2	MCF-7	breast:
20	chr1:227973508..227976414-chr1:228271906..228274660,2	K562	blood:

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000162913	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000081692	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000173334	Chromatin interaction
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12022027	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12022323	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12023551	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12024368	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12026579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12028729	1.00[AFR][1000 genomes]
rs12028894	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12029540	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12030528	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12031017	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12031390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12031747	0.85[AMR][1000 genomes]
rs12032905	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12033588	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12033624	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12036485	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12037964	0.85[AMR][1000 genomes]
rs12038090	0.85[AMR][1000 genomes]
rs12038612	1.00[AMR][1000 genomes]
rs12039528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12040506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12043464	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12044962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12048283	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12049152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12120597	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1411913	1.00[CHB][hapmap]
rs16848197	0.83[AMR][1000 genomes]
rs1934882	1.00[CHB][hapmap]
rs2298013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28603121	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3754359	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]
rs55760713	0.85[AMR][1000 genomes]
rs55946300	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56154605	0.85[AMR][1000 genomes]
rs56384735	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs74140905	0.92[AMR][1000 genomes]
rs74140962	0.92[AMR][1000 genomes]
rs74140968	0.92[AMR][1000 genomes]
rs74140985	0.92[AMR][1000 genomes]
rs74143629	0.92[AMR][1000 genomes]
rs74143633	0.85[AMR][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	chr1:228269200-228272000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:228269200-228272000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:228269200-228272200	Active TSS	Right Atrium	heart
5	chr1:228269200-228272400	Active TSS	NHLF	lung
6	chr1:228269400-228272000	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:228269400-228272000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:228269400-228272000	Active TSS	NH-A	brain
9	chr1:228269400-228272400	Active TSS	HSMM	muscle
10	chr1:228269400-228272600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:228269600-228272000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:228269600-228272000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:228269600-228272000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:228269600-228272000	Active TSS	Fetal Intestine Large	intestine
15	chr1:228269600-228272000	Active TSS	Stomach Mucosa	stomach
16	chr1:228269600-228272200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:228269600-228272200	Active TSS	Gastric	stomach
18	chr1:228269600-228272200	Active TSS	Ovary	ovary
19	chr1:228269600-228272200	Active TSS	Small Intestine	intestine
20	chr1:228269600-228272400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:228269600-228272400	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr1:228269600-228272400	Active TSS	Aorta	Aorta
23	chr1:228269600-228272400	Active TSS	HSMMtube	muscle
24	chr1:228269600-228272400	Active TSS	NHDF-Ad	bronchial
25	chr1:228269600-228272600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:228269600-228272600	Active TSS	Lung	lung
27	chr1:228269600-228272600	Active TSS	Psoas Muscle	Psoas
28	chr1:228269800-228272000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:228270200-228272400	Active TSS	Fetal Muscle Trunk	muscle
30	chr1:228270800-228272200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:228271000-228272000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:228271000-228272000	Transcr. at gene 5' and 3'	Fetal Lung	lung
33	chr1:228271000-228272200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:228271000-228272200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr1:228271000-228272800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr1:228271000-228273000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:228271000-228273400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:228271000-228273600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:228271000-228273600	Transcr. at gene 5' and 3'	Dnd41	blood
40	chr1:228271000-228273800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:228271000-228274000	Flanking Active TSS	Stomach Smooth Muscle	stomach
42	chr1:228271200-228272000	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:228271200-228272000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr1:228271200-228272200	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr1:228271200-228272200	Transcr. at gene 5' and 3'	Thymus	Thymus
46	chr1:228271200-228272400	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr1:228271200-228272400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr1:228271200-228272400	Flanking Active TSS	Brain Germinal Matrix	brain
49	chr1:228271200-228272600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:228271200-228272800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links