Variant report

Variant	rs74142611
Chromosome Location	chr1:228352082-228352083
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228350764-228354251	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:228351608-228352093	K562	blood:	n/a	n/a
3	MAX	chr1:228352049-228352833	K562	blood:	n/a	n/a
4	POLR2A	chr1:228352004-228354681	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:228352002-228352194	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:228351371-228354514	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:228351959-228354520	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:228350272-228354541	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr1:228351957-228352157	K562	blood:	n/a	n/a
10	POLR2A	chr1:228351978-228352096	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr1:228352032-228352433	HepG2	liver:	n/a	n/a
12	POLR2A	chr1:228351886-228352438	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:228348937-228354538	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:228352022-228352727	HL-60	blood:	n/a	n/a
15	PML	chr1:228352054-228352649	K562	blood:	n/a	n/a
16	HDAC2	chr1:228352065-228352685	K562	blood:	n/a	n/a
17	POLR2A	chr1:228352067-228352812	K562	blood:	n/a	n/a
18	NR2F2	chr1:228352066-228354805	K562	blood:	n/a	n/a
19	POLR2A	chr1:228351991-228352328	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr1:228349847-228354537	MCF10A-Er-Src	breast:	n/a	n/a
21	RCOR1	chr1:228351943-228353723	K562	blood:	n/a	n/a
22	POLR2A	chr1:228351854-228353656	K562	blood:	n/a	n/a
23	POLR2A	chr1:228349182-228354536	Hela-S3	cervix:	n/a	n/a
24	JUN	chr1:228352007-228355103	K562	blood:	n/a	chr1:228353288-228353297 chr1:228353839-228353852 chr1:228353424-228353433
25	POLR2A	chr1:228352031-228352749	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr1:228351455-228354172	SK-N-MC	brain:	n/a	n/a
27	HDAC2	chr1:228352046-228352558	K562	blood:	n/a	n/a
28	POLR2A	chr1:228349204-228352644	Raji	blood:	n/a	n/a
29	POLR2A	chr1:228351628-228354510	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228288054..228293498-chr1:228351743..228355627,9	K562	blood:
2	chr1:228351819..228355005-chr1:228461791..228464668,3	K562	blood:
3	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
4	chr1:228351867..228354707-chr1:228644066..228646838,3	K562	blood:
5	chr1:228349528..228352253-chr1:228378425..228381248,2	MCF-7	breast:
6	chr1:16839413..16842020-chr1:228351900..228354704,2	K562	blood:
7	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
8	chr1:228351767..228353945-chr1:228395258..228397219,2	MCF-7	breast:
9	chr1:228268894..228271778-chr1:228351302..228354925,4	MCF-7	breast:
10	chr1:228295286..228298610-chr1:228351640..228355026,4	K562	blood:
11	chr1:228350980..228355955-chr1:228356979..228359321,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf148-1	chr1:228351787-228352193	NR_103540
2	lnc-C1orf148-1	chr1:228351787-228352193	NONHSAT009994

No data

Variant related genes	Relation type
IBA57	TF binding region
ENSG00000269934	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000261135	Chromatin interaction
ENSG00000269890	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000206652	Chromatin interaction
ENSG00000143793	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]
rs74142610	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:104 , 50 per page) page: 1 2 3

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	chr1:228349000-228352200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr1:228349000-228352800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:228349000-228352800	Enhancers	Placenta	Placenta
11	chr1:228349200-228352800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:228349200-228352800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:228349200-228352800	Enhancers	Pancreas	Pancrea
14	chr1:228349200-228352800	Enhancers	Right Ventricle	heart
15	chr1:228349200-228352800	Enhancers	HMEC	breast
16	chr1:228349200-228352800	Enhancers	HUVEC	blood vessel
17	chr1:228349400-228352600	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:228349600-228352200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:228349600-228352800	Enhancers	Psoas Muscle	Psoas
20	chr1:228349600-228352800	Enhancers	Spleen	Spleen
21	chr1:228350000-228352200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:228350200-228352800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:228350200-228352800	Flanking Active TSS	Hela-S3	cervix
24	chr1:228350400-228352600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:228350400-228352800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:228350400-228352800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:228350400-228352800	Enhancers	Fetal Muscle Leg	muscle
28	chr1:228350400-228352800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:228350600-228352400	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:228350600-228352400	Weak transcription	Thymus	Thymus
31	chr1:228350600-228352600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:228350600-228352600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:228350600-228352600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:228350600-228352800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:228350600-228352800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:228350800-228352200	Weak transcription	Primary B cells from cord blood	blood
37	chr1:228350800-228352200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:228350800-228352200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:228350800-228352400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:228350800-228352400	Weak transcription	Fetal Lung	lung
41	chr1:228350800-228352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:228350800-228352800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:228350800-228352800	Weak transcription	Left Ventricle	heart
44	chr1:228350800-228352800	Weak transcription	Ovary	ovary
45	chr1:228351000-228352200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:228351000-228352400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:228351000-228352400	Weak transcription	Right Atrium	heart
48	chr1:228351000-228352400	Enhancers	HepG2	liver
49	chr1:228351000-228352600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:228351000-228352600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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