Variant report

Variant	rs74142608
Chromosome Location	chr1:228349283-228349284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228349254-228349288	Gliobla	brain:	n/a	n/a
2	CEBPB	chr1:228349274-228349353	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:228348821-228349486	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr1:228349200-228349350	HEEpiC	esophagus:	n/a	n/a
5	POLR2A	chr1:228349134-228349506	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:228349082-228351793	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr1:228349141-228349341	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:228348937-228354538	MCF10A-Er-Src	breast:	n/a	n/a
9	SMC3	chr1:228349116-228349320	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:228349077-228349422	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:228349207-228349513	K562	blood:	n/a	n/a
12	POLR2A	chr1:228349182-228354536	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:228349226-228349390	MCF-7	breast:	n/a	n/a
14	POLR2A	chr1:228349187-228351129	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr1:228349143-228349364	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:228349117-228349868	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:228349261-228349353	K562	blood:	n/a	n/a
18	POLR2A	chr1:228349204-228352644	Raji	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228349005..228351267-chr1:228399085..228402017,2	MCF-7	breast:
2	chr1:228347944..228349967-chr1:228460041..228462528,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GJC2-1	chr1:228348810-228349358	NONHSAT009993

No data

Variant related genes	Relation type
IBA57	TF binding region
ENSG00000162913	Chromatin interaction
ENSG00000269890	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs15109	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16848270	0.90[ASN][1000 genomes]
rs55662277	1.00[AFR][1000 genomes]
rs55686465	0.90[ASN][1000 genomes]
rs55904630	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55923168	0.90[ASN][1000 genomes]
rs56003736	0.90[ASN][1000 genomes]
rs56029925	0.90[ASN][1000 genomes]
rs56080014	1.00[ASN][1000 genomes]
rs56137152	0.85[AFR][1000 genomes]
rs56280722	1.00[AFR][1000 genomes]
rs56285667	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56377909	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56386805	1.00[AFR][1000 genomes]
rs56410225	1.00[AFR][1000 genomes]
rs56831205	0.90[ASN][1000 genomes]
rs57446195	0.90[ASN][1000 genomes]
rs58045861	1.00[ASN][1000 genomes]
rs59460700	1.00[AFR][1000 genomes]
rs59478442	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60245137	0.90[ASN][1000 genomes]
rs60628313	0.86[AFR][1000 genomes]
rs61100243	1.00[AFR][1000 genomes]
rs61230585	0.90[ASN][1000 genomes]
rs61401568	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61737797	0.90[ASN][1000 genomes]
rs74140907	0.90[ASN][1000 genomes]
rs74140910	0.90[ASN][1000 genomes]
rs74140912	0.90[ASN][1000 genomes]
rs74140915	0.90[ASN][1000 genomes]
rs74140916	0.90[ASN][1000 genomes]
rs74140918	0.90[ASN][1000 genomes]
rs74140919	0.90[ASN][1000 genomes]
rs74140923	0.90[ASN][1000 genomes]
rs74140925	0.90[ASN][1000 genomes]
rs74140953	0.90[ASN][1000 genomes]
rs74140954	0.90[ASN][1000 genomes]
rs74140955	0.90[ASN][1000 genomes]
rs74140956	0.90[ASN][1000 genomes]
rs74140957	0.90[ASN][1000 genomes]
rs74140960	0.90[ASN][1000 genomes]
rs74140961	0.90[ASN][1000 genomes]
rs74140963	0.90[ASN][1000 genomes]
rs74140965	0.90[ASN][1000 genomes]
rs74140967	0.90[ASN][1000 genomes]
rs74140969	0.81[ASN][1000 genomes]
rs74140970	1.00[ASN][1000 genomes]
rs74140973	1.00[ASN][1000 genomes]
rs74140976	1.00[ASN][1000 genomes]
rs74140978	1.00[ASN][1000 genomes]
rs74140980	1.00[ASN][1000 genomes]
rs74140986	1.00[AFR][1000 genomes]
rs74140987	1.00[AFR][1000 genomes]
rs74140988	1.00[AFR][1000 genomes]
rs74140989	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140990	1.00[AFR][1000 genomes]
rs74140994	1.00[ASN][1000 genomes]
rs74140996	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74141000	1.00[AFR][1000 genomes]
rs74141002	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74142604	1.00[AFR][1000 genomes]
rs74142605	1.00[AFR][1000 genomes]
rs74142606	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74142610	1.00[AFR][1000 genomes]
rs74142611	1.00[AFR][1000 genomes]
rs74142613	1.00[AFR][1000 genomes]
rs74142616	1.00[AFR][1000 genomes]
rs74142618	1.00[AFR][1000 genomes]
rs74142619	1.00[AFR][1000 genomes]
rs74142622	1.00[AFR][1000 genomes]
rs74142624	0.85[AFR][1000 genomes]
rs74142625	1.00[ASN][1000 genomes]
rs74142626	0.85[AFR][1000 genomes]
rs74142627	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74142629	0.85[AFR][1000 genomes]
rs74142630	0.85[AFR][1000 genomes]
rs74142638	0.85[AFR][1000 genomes]
rs74142640	0.85[AFR][1000 genomes]
rs74142642	1.00[ASN][1000 genomes]
rs74142644	1.00[ASN][1000 genomes]
rs74142645	1.00[ASN][1000 genomes]
rs74142647	1.00[ASN][1000 genomes]
rs74143631	0.90[ASN][1000 genomes]
rs74143632	0.90[ASN][1000 genomes]
rs74143634	0.90[ASN][1000 genomes]
rs74143635	0.90[ASN][1000 genomes]
rs74143636	0.90[ASN][1000 genomes]
rs74143637	0.90[ASN][1000 genomes]
rs74143638	0.90[ASN][1000 genomes]
rs74143640	0.90[ASN][1000 genomes]
rs74143641	0.90[ASN][1000 genomes]
rs74143642	0.90[ASN][1000 genomes]
rs74143662	0.90[ASN][1000 genomes]
rs74143665	0.90[ASN][1000 genomes]
rs74143667	0.90[ASN][1000 genomes]
rs752108	0.90[ASN][1000 genomes]
rs752109	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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
17	nsv549291	chr1:228338939-228350774	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	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
19	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
20	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
21	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
22	nsv827031	chr1:228344082-228349790	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228332800-228349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:228333800-228350400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:228336800-228350200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:228337800-228349800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:228338000-228349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:228338200-228352400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:228339400-228352600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:228339800-228349400	Weak transcription	Brain Angular Gyrus	brain
9	chr1:228340600-228349600	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:228342600-228350000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:228343400-228352400	Weak transcription	A549	lung
12	chr1:228344200-228352200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:228345400-228349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:228345400-228349800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:228345800-228349400	Weak transcription	Primary T cells from cord blood	blood
16	chr1:228345800-228349400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:228345800-228349800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:228345800-228351400	Enhancers	Esophagus	oesophagus
19	chr1:228346000-228349400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:228346200-228349800	Weak transcription	Thymus	Thymus
21	chr1:228346400-228349600	Weak transcription	Right Atrium	heart
22	chr1:228346600-228350000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:228346800-228349600	Weak transcription	Psoas Muscle	Psoas
24	chr1:228347000-228349600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:228347000-228349600	Weak transcription	Spleen	Spleen
26	chr1:228347200-228350000	Weak transcription	Ovary	ovary
27	chr1:228347400-228350000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:228347400-228350000	Enhancers	NHEK	skin
29	chr1:228348400-228350200	Enhancers	Hela-S3	cervix
30	chr1:228348600-228349600	Bivalent Enhancer	Fetal Intestine Small	intestine
31	chr1:228348600-228349800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr1:228348600-228350200	Enhancers	HepG2	liver
33	chr1:228348600-228350800	Enhancers	Left Ventricle	heart
34	chr1:228348600-228352600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:228348600-228352800	Enhancers	Fetal Thymus	thymus
36	chr1:228348600-228352800	Enhancers	Lung	lung
37	chr1:228348800-228349800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:228348800-228350400	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr1:228348800-228351000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:228348800-228351800	Enhancers	Fetal Intestine Large	intestine
41	chr1:228349000-228349600	Enhancers	Brain Substantia Nigra	brain
42	chr1:228349000-228349800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:228349000-228350600	Enhancers	Brain Hippocampus Middle	brain
44	chr1:228349000-228351200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr1:228349000-228351200	Enhancers	NHLF	lung
46	chr1:228349000-228351600	Enhancers	Gastric	stomach
47	chr1:228349000-228352200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr1:228349000-228352800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr1:228349000-228352800	Enhancers	Placenta	Placenta
50	chr1:228349200-228349400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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