Variant report

Variant	rs55662277
Chromosome Location	chr1:228337035-228337036
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	chr1:228336621-228339727	A549	lung:	n/a	n/a
2	POLR2A	chr1:228336020-228337761	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr1:228336912-228337663	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:228336769-228338464	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:228337018-228337810	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:228336815-228339194	HepG2	liver:	n/a	n/a
7	TFAP2C	chr1:228336626-228337754	Hela-S3	cervix:	n/a	chr1:228336931-228336946 chr1:228337424-228337439 chr1:228336910-228336925
8	POLR2A	chr1:228336707-228338965	K562	blood:	n/a	n/a
9	POLR2A	chr1:228332644-228338827	K562	blood:	n/a	n/a
10	POLR2A	chr1:228336745-228339203	GM12892	blood:	n/a	n/a
11	HMGN3	chr1:228336768-228337609	K562	blood:	n/a	n/a
12	POLR2A	chr1:228336697-228337353	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:228337010-228337587	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:228336623-228337717	K562	blood:	n/a	n/a
15	POLR2A	chr1:228337026-228337449	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:228336709-228339558	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:228336471-228339512	K562	blood:	n/a	n/a
18	POLR2A	chr1:228336675-228337354	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:228336841-228339585	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr1:228336803-228339922	IMR90	lung:	n/a	n/a
21	POLR2A	chr1:228336652-228338674	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:228336859-228337797	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:228336174-228339596	K562	blood:	n/a	n/a
24	POLR2A	chr1:228335762-228339602	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:228336594-228337252	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:228337018-228337659	PANC-1	pancreas:	n/a	n/a
27	ZBTB7A	chr1:228336995-228337633	K562	blood:	n/a	n/a
28	POLR2A	chr1:228336527-228337307	GM12892	blood:	n/a	n/a
29	CBX3	chr1:228336946-228337585	K562	blood:	n/a	n/a
30	POLR2A	chr1:228336601-228337713	K562	blood:	n/a	n/a
31	MAZ	chr1:228336865-228339350	IMR90	lung:	n/a	chr1:228339173-228339182 chr1:228339174-228339181 chr1:228339172-228339182 chr1:228339172-228339182 chr1:228339173-228339182 chr1:228338104-228338114 chr1:228339171-228339186
32	POLR2A	chr1:228336612-228338002	K562	blood:	n/a	n/a
33	POLR2A	chr1:228335884-228339752	GM12878	blood:	n/a	n/a
34	MYBL2	chr1:228337035-228337489	HepG2	liver:	n/a	n/a
35	ZNF263	chr1:228337010-228337271	HEK293-T-REx	kidney:	n/a	chr1:228337128-228337149 chr1:228337131-228337140
36	ZNF263	chr1:228336898-228337491	K562	blood:	n/a	chr1:228337128-228337149 chr1:228337131-228337140
37	POLR2A	chr1:228336657-228338786	GM12878	blood:	n/a	n/a
38	POLR2A	chr1:228336995-228337749	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228295623..228298108-chr1:228335544..228338438,2	MCF-7	breast:
2	chr1:228267816..228271023-chr1:228334433..228337364,3	K562	blood:
3	chr1:228270474..228272694-chr1:228336357..228338344,2	K562	blood:
4	chr1:228291320..228293457-chr1:228336716..228339227,2	K562	blood:

Variant related genes	Relation type
GJC2	TF binding region
ENSG00000143793	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11541554	1.00[AMR][1000 genomes]
rs15109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2231717	1.00[AMR][1000 genomes]
rs55686465	1.00[AMR][1000 genomes]
rs55904630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55923168	1.00[AMR][1000 genomes]
rs56003736	1.00[AMR][1000 genomes]
rs56029925	1.00[AMR][1000 genomes]
rs56080014	1.00[AMR][1000 genomes]
rs56137152	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56280722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56285667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56377909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56386805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56410225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58045861	1.00[AMR][1000 genomes]
rs59460700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59478442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60628313	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61100243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61230585	1.00[AMR][1000 genomes]
rs61401568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140910	1.00[AMR][1000 genomes]
rs74140916	1.00[AMR][1000 genomes]
rs74140919	1.00[AMR][1000 genomes]
rs74140923	1.00[AMR][1000 genomes]
rs74140953	1.00[AMR][1000 genomes]
rs74140954	1.00[AMR][1000 genomes]
rs74140955	1.00[AMR][1000 genomes]
rs74140956	1.00[AMR][1000 genomes]
rs74140957	1.00[AMR][1000 genomes]
rs74140963	1.00[AMR][1000 genomes]
rs74140967	1.00[AMR][1000 genomes]
rs74140969	1.00[AMR][1000 genomes]
rs74140970	1.00[AMR][1000 genomes]
rs74140971	1.00[AMR][1000 genomes]
rs74140972	1.00[AMR][1000 genomes]
rs74140973	1.00[AMR][1000 genomes]
rs74140974	1.00[AMR][1000 genomes]
rs74140975	1.00[AMR][1000 genomes]
rs74140976	1.00[AMR][1000 genomes]
rs74140977	1.00[AMR][1000 genomes]
rs74140978	1.00[AMR][1000 genomes]
rs74140980	1.00[AMR][1000 genomes]
rs74140981	1.00[AMR][1000 genomes]
rs74140982	1.00[AMR][1000 genomes]
rs74140986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140999	1.00[AMR][1000 genomes]
rs74141000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74141002	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142608	1.00[AFR][1000 genomes]
rs74142610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142616	1.00[AFR][1000 genomes]
rs74142618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142624	0.85[AFR][1000 genomes]
rs74142626	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142627	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142629	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142630	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142638	0.85[AFR][1000 genomes]
rs74142640	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
9	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
10	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
11	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
13	nsv549290	chr1:228333652-228349806	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv873258	chr1:228334088-228359775	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv873259	chr1:228334277-228359775	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
16	nsv873260	chr1:228334277-228371098	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228329000-228339400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:228329000-228339600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:228329200-228337400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:228329400-228337600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:228329400-228337600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:228329400-228338200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:228330000-228337200	Genic enhancers	Fetal Muscle Leg	muscle
8	chr1:228330000-228337800	Genic enhancers	Lung	lung
9	chr1:228330600-228337200	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr1:228331000-228338800	Weak transcription	HSMMtube	muscle
11	chr1:228331400-228341800	Weak transcription	Psoas Muscle	Psoas
12	chr1:228331600-228341000	Genic enhancers	Fetal Thymus	thymus
13	chr1:228332200-228337400	Strong transcription	Dnd41	blood
14	chr1:228332400-228337200	Genic enhancers	Esophagus	oesophagus
15	chr1:228332400-228339400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:228332600-228337600	Weak transcription	Small Intestine	intestine
17	chr1:228332600-228338200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:228332800-228337800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:228332800-228338200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr1:228332800-228339000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr1:228332800-228349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:228333000-228337200	Strong transcription	Liver	Liver
23	chr1:228333000-228337400	Strong transcription	Brain Germinal Matrix	brain
24	chr1:228333000-228337800	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr1:228333000-228338000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:228333200-228337200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:228333200-228337400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
28	chr1:228333200-228337800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:228333200-228337800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:228333200-228337800	Strong transcription	Fetal Brain Female	brain
31	chr1:228333200-228338000	Genic enhancers	Right Ventricle	heart
32	chr1:228333200-228342200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:228333200-228344600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:228333400-228337200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:228333400-228338200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:228333600-228338200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:228333800-228337800	Strong transcription	Thymus	Thymus
38	chr1:228333800-228350400	Weak transcription	Primary B cells from cord blood	blood
39	chr1:228334200-228340000	Genic enhancers	Spleen	Spleen
40	chr1:228334800-228338800	Weak transcription	Aorta	Aorta
41	chr1:228335600-228338000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr1:228335600-228338400	Weak transcription	GM12878-XiMat	blood
43	chr1:228335800-228337400	Genic enhancers	Fetal Stomach	stomach
44	chr1:228335800-228337400	Genic enhancers	NHLF	lung
45	chr1:228335800-228338000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:228335800-228338200	Genic enhancers	Placenta	Placenta
47	chr1:228335800-228339600	Enhancers	Right Atrium	heart
48	chr1:228335800-228339800	Enhancers	Fetal Lung	lung
49	chr1:228336000-228337200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:228336000-228337200	Genic enhancers	Gastric	stomach

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