Variant report

Variant	rs74142610
Chromosome Location	chr1:228351533-228351534
allele	G/T
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	TFAP2C	chr1:228350071-228351707	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:228350764-228354251	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:228351494-228351928	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:228351371-228354514	GM12891	blood:	n/a	n/a
5	FOS	chr1:228351404-228351603	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:228350272-228354541	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:228349082-228351793	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:228348937-228354538	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:228349847-228354537	MCF10A-Er-Src	breast:	n/a	n/a
10	TFAP2A	chr1:228350071-228351899	Hela-S3	cervix:	n/a	chr1:228350324-228350338 chr1:228350943-228350954 chr1:228351337-228351349 chr1:228350755-228350763 chr1:228350943-228350954 chr1:228351337-228351349 chr1:228350755-228350763 chr1:228351337-228351349 chr1:228350942-228350957 chr1:228350944-228350952 chr1:228350944-228350952 chr1:228350324-228350338 chr1:228350755-228350763 chr1:228351337-228351351 chr1:228350324-228350338 chr1:228351337-228351349 chr1:228350944-228350952
11	POLR2A	chr1:228349182-228354536	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:228351455-228354172	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr1:228349204-228352644	Raji	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
2	chr1:228349528..228352253-chr1:228378425..228381248,2	MCF-7	breast:
3	chr1:228268894..228271778-chr1:228351302..228354925,4	MCF-7	breast:
4	chr1:228350980..228355955-chr1:228356979..228359321,5	MCF-7	breast:

Variant related genes	Relation type
IBA57	TF binding region
ENSG00000143761	Chromatin interaction
ENSG00000181873	Chromatin interaction

Extended variants
information (count: 92 )
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]
rs55662277	1.00[AFR][1000 genomes];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]
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:19 , 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	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
14	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
15	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
16	nsv873261	chr1:228338939-228359775	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
17	nsv873262	chr1:228340653-228371098	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
18	nsv1012078	chr1:228340876-228521843	Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
19	nsv535320	chr1:228340876-228521843	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228338200-228352400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228339400-228352600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:228343400-228352400	Weak transcription	A549	lung
4	chr1:228344200-228352200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:228348600-228352600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr1:228348600-228352800	Enhancers	Fetal Thymus	thymus
7	chr1:228348600-228352800	Enhancers	Lung	lung
8	chr1:228348800-228351800	Enhancers	Fetal Intestine Large	intestine
9	chr1:228349000-228351600	Enhancers	Gastric	stomach
10	chr1:228349000-228352200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
11	chr1:228349000-228352800	Enhancers	Primary T cells fromperipheralblood	blood
12	chr1:228349000-228352800	Enhancers	Placenta	Placenta
13	chr1:228349200-228351600	Enhancers	Duodenum Mucosa	Duodenum
14	chr1:228349200-228351600	Enhancers	Fetal Heart	heart
15	chr1:228349200-228352800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:228349200-228352800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:228349200-228352800	Enhancers	Pancreas	Pancrea
18	chr1:228349200-228352800	Enhancers	Right Ventricle	heart
19	chr1:228349200-228352800	Enhancers	HMEC	breast
20	chr1:228349200-228352800	Enhancers	HUVEC	blood vessel
21	chr1:228349400-228351600	Enhancers	HSMMtube	muscle
22	chr1:228349400-228352600	Enhancers	Primary hematopoietic stem cells	blood
23	chr1:228349600-228351600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:228349600-228351800	Enhancers	Fetal Intestine Small	intestine
25	chr1:228349600-228352200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:228349600-228352800	Enhancers	Psoas Muscle	Psoas
27	chr1:228349600-228352800	Enhancers	Spleen	Spleen
28	chr1:228350000-228351600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:228350000-228351600	Enhancers	NH-A	brain
30	chr1:228350000-228351800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:228350000-228351800	Flanking Active TSS	NHEK	skin
32	chr1:228350000-228352200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:228350200-228352800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:228350200-228352800	Flanking Active TSS	Hela-S3	cervix
35	chr1:228350400-228352000	Weak transcription	Primary B cells from peripheral blood	blood
36	chr1:228350400-228352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:228350400-228352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:228350400-228352800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:228350400-228352800	Enhancers	Fetal Muscle Leg	muscle
40	chr1:228350400-228352800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:228350600-228351600	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr1:228350600-228352400	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:228350600-228352400	Weak transcription	Thymus	Thymus
44	chr1:228350600-228352600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:228350600-228352600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:228350600-228352600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:228350600-228352800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:228350600-228352800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:228350800-228351800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:228350800-228351800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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