Variant report

Variant	rs74140962
Chromosome Location	chr1:228292701-228292702
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:50 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228290521-228294679	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr1:228292533-228293154	Raji	blood:	n/a	n/a
3	POLR2A	chr1:228292437-228293997	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:228284138-228294734	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:228292566-228293234	A549	lung:	n/a	n/a
6	POLR2A	chr1:228291771-228293318	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:228292587-228292856	HCT-116	colon:	n/a	n/a
8	POLR2A	chr1:228290729-228294672	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:228292241-228293966	K562	blood:	n/a	n/a
10	POLR2A	chr1:228291694-228293754	GM12891	blood:	n/a	n/a
11	POLR2A	chr1:228292585-228293264	A549	lung:	n/a	n/a
12	POLR2A	chr1:228292210-228292959	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:228291721-228293245	K562	blood:	n/a	n/a
14	POLR2A	chr1:228292597-228293250	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:228292600-228293137	HCT-116	colon:	n/a	n/a
16	POLR2A	chr1:228290784-228293701	K562	blood:	n/a	n/a
17	POLR2A	chr1:228292699-228292713	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr1:228292601-228293240	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:228292295-228293417	HL-60	blood:	n/a	n/a
20	POLR2A	chr1:228291793-228293277	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:228292668-228292766	ProgFib	skin:	n/a	n/a
22	POLR2A	chr1:228291713-228293928	K562	blood:	n/a	n/a
23	POLR2A	chr1:228283726-228293977	K562	blood:	n/a	n/a
24	POLR2A	chr1:228291590-228293576	HEK293	kidney:	n/a	n/a
25	POLR2A	chr1:228291974-228292793	U87	brain:	n/a	n/a
26	POLR2A	chr1:228291632-228294040	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr1:228292593-228293260	PANC-1	pancreas:	n/a	n/a
28	POLR2A	chr1:228292544-228293316	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:228290539-228293307	GM12892	blood:	n/a	n/a
30	POLR2A	chr1:228289866-228293896	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:228291595-228294465	HepG2	liver:	n/a	n/a
32	CHD2	chr1:228292671-228292815	K562	blood:	n/a	n/a
33	POLR2A	chr1:228290818-228294408	K562	blood:	n/a	n/a
34	POLR2A	chr1:228291654-228293974	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:228292393-228292780	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:228292668-228292901	MCF-7	breast:	n/a	n/a
37	HEY1	chr1:228292592-228292910	K562	blood:	n/a	n/a
38	POLR2A	chr1:228292534-228293261	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:228292617-228292955	A549	lung:	n/a	n/a
40	POLR2A	chr1:228292653-228292923	A549	lung:	n/a	n/a
41	POLR2A	chr1:228292513-228292965	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:228292256-228293010	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr1:228292664-228292907	A549	lung:	n/a	n/a
44	POLR2A	chr1:228292538-228293035	GM12892	blood:	n/a	n/a
45	POLR2A	chr1:228291406-228294664	K562	blood:	n/a	n/a
46	POLR2A	chr1:228292569-228293822	HepG2	liver:	n/a	n/a
47	POLR2A	chr1:228292580-228292975	MCF-7	breast:	n/a	n/a
48	POLR2A	chr1:228290793-228293227	GM12891	blood:	n/a	n/a
49	POLR2A	chr1:228292365-228294372	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:228292475-228293191	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228290240..228294197-chr1:228325970..228329742,3	MCF-7	breast:
2	chr1:228291284..228293085-chr1:228340318..228343029,2	K562	blood:
3	chr1:228291320..228293457-chr1:228336716..228339227,2	K562	blood:
4	chr1:228290061..228293195-chr1:228643504..228645569,3	K562	blood:
5	chr1:228290240..228293064-chr1:228675062..228676582,2	K562	blood:
6	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
7	chr1:228288054..228293498-chr1:228351743..228355627,9	K562	blood:
8	chr1:228288649..228293430-chr1:228325997..228329591,7	K562	blood:

No data

Variant related genes	Relation type
C1orf35	TF binding region
ENSG00000168159	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000181218	Chromatin interaction

Extended variants
information (count: 55 )
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	0.92[AMR][1000 genomes]
rs3754359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][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]
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:11 , 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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228291400-228292800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:228291400-228292800	Enhancers	Pancreas	Pancrea
3	chr1:228291400-228293400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:228291400-228296400	Weak transcription	Aorta	Aorta
5	chr1:228291600-228293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:228291600-228293000	Weak transcription	Esophagus	oesophagus
7	chr1:228291600-228293000	Weak transcription	Gastric	stomach
8	chr1:228291600-228293000	Enhancers	Left Ventricle	heart
9	chr1:228291600-228293000	Weak transcription	Ovary	ovary
10	chr1:228291600-228293000	Enhancers	Right Ventricle	heart
11	chr1:228291600-228293200	Enhancers	Liver	Liver
12	chr1:228291600-228293400	Weak transcription	Lung	lung
13	chr1:228291600-228296000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:228291800-228292800	Enhancers	Colon Smooth Muscle	Colon
15	chr1:228291800-228292800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr1:228291800-228292800	Enhancers	Fetal Heart	heart
17	chr1:228291800-228293000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:228291800-228293000	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:228291800-228293000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:228291800-228293000	Enhancers	Fetal Muscle Leg	muscle
21	chr1:228291800-228293000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:228291800-228293000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:228291800-228293600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:228291800-228293600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:228291800-228293600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:228291800-228293600	Weak transcription	Stomach Mucosa	stomach
27	chr1:228291800-228293800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:228291800-228293800	Weak transcription	HSMMtube	muscle
29	chr1:228291800-228294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:228291800-228294000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:228291800-228294000	Weak transcription	HMEC	breast
32	chr1:228291800-228295600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:228291800-228295600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:228291800-228296200	Weak transcription	NH-A	brain
35	chr1:228291800-228296400	Weak transcription	Small Intestine	intestine
36	chr1:228292000-228292800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:228292000-228292800	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr1:228292000-228292800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:228292000-228292800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:228292000-228292800	Enhancers	Adipose Nuclei	Adipose
41	chr1:228292000-228292800	Enhancers	NHDF-Ad	bronchial
42	chr1:228292000-228292800	Weak transcription	NHLF	lung
43	chr1:228292000-228293000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:228292000-228293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:228292000-228293200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:228292000-228293400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:228292000-228293400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:228292000-228293400	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:228292000-228293400	Weak transcription	Brain Substantia Nigra	brain
50	chr1:228292000-228293400	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links