Variant report

Variant	rs74140925
Chromosome Location	chr1:228276720-228276721
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	chr1:228274276-228290284	K562	blood:	n/a	n/a
2	POLR2A	chr1:228274933-228281306	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:228276440-228276790	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:228276335-228278744	K562	blood:	n/a	n/a
5	POLR2A	chr1:228275627-228277219	HL-60	blood:	n/a	n/a
6	POLR2A	chr1:228276252-228277126	K562	blood:	n/a	n/a
7	POLR2A	chr1:228276238-228276822	HL-60	blood:	n/a	n/a
8	POLR2A	chr1:228276702-228277001	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:228276242-228277221	GM12892	blood:	n/a	n/a
10	POLR2A	chr1:228276265-228276982	PFSK-1	brain:	n/a	n/a
11	HEY1	chr1:228276650-228277082	K562	blood:	n/a	chr1:228276650-228276665
12	POLR2A	chr1:228276425-228276867	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:228276358-228278146	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:228276225-228279615	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr1:228276638-228276766	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:228276273-228277102	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:228274170-228289426	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:228276294-228277180	K562	blood:	n/a	n/a
19	POLR2A	chr1:228276366-228280674	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:228276326-228278305	K562	blood:	n/a	n/a
21	EBF1	chr1:228276441-228277636	GM12878	blood:	n/a	chr1:228276981-228276990 chr1:228276968-228276979
22	POLR2A	chr1:228276334-228277960	GM12891	blood:	n/a	n/a
23	POLR2A	chr1:228276329-228277113	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:228276285-228277148	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:228276275-228279657	K562	blood:	n/a	n/a
26	WRNIP1	chr1:228276397-228277961	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:228275014-228282866	GM12878	blood:	n/a	n/a
28	HEY1	chr1:228276266-228277029	K562	blood:	n/a	chr1:228276650-228276665
29	POLR2A	chr1:228276361-228281309	A549	lung:	n/a	n/a
30	POLR2A	chr1:228274271-228281353	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:228276610-228276725	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr1:228276367-228276943	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228274118..228278669-chr1:228294195..228297645,6	MCF-7	breast:
2	chr1:228275922..228277481-chr1:228353346..228356104,2	MCF-7	breast:
3	chr1:228275377..228276887-chr1:228353250..228355389,2	K562	blood:

Variant related genes	Relation type
ARF1	TF binding region
ENSG00000181873	Chromatin interaction
ENSG00000162910	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs15109	0.90[ASN][1000 genomes]
rs16848270	1.00[ASN][1000 genomes]
rs55686465	1.00[ASN][1000 genomes]
rs55904630	0.90[ASN][1000 genomes]
rs55923168	1.00[ASN][1000 genomes]
rs55954688	1.00[AFR][1000 genomes]
rs56003736	1.00[ASN][1000 genomes]
rs56029925	1.00[ASN][1000 genomes]
rs56080014	0.90[ASN][1000 genomes]
rs56226852	1.00[AFR][1000 genomes]
rs56285667	0.90[ASN][1000 genomes]
rs56377909	0.90[ASN][1000 genomes]
rs56831205	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57446195	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57450243	1.00[AFR][1000 genomes]
rs58035269	1.00[AFR][1000 genomes]
rs58045861	0.90[ASN][1000 genomes]
rs59478442	0.90[ASN][1000 genomes]
rs60245137	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61230585	1.00[ASN][1000 genomes]
rs61401568	0.90[ASN][1000 genomes]
rs61737797	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140907	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140910	1.00[ASN][1000 genomes]
rs74140912	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140914	1.00[AFR][1000 genomes]
rs74140915	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140916	1.00[ASN][1000 genomes]
rs74140918	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140919	1.00[ASN][1000 genomes]
rs74140923	1.00[ASN][1000 genomes]
rs74140924	1.00[AFR][1000 genomes]
rs74140953	1.00[ASN][1000 genomes]
rs74140954	1.00[ASN][1000 genomes]
rs74140955	1.00[ASN][1000 genomes]
rs74140956	1.00[ASN][1000 genomes]
rs74140957	1.00[ASN][1000 genomes]
rs74140960	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140961	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140963	1.00[ASN][1000 genomes]
rs74140965	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74140967	1.00[ASN][1000 genomes]
rs74140969	0.90[ASN][1000 genomes]
rs74140970	0.90[ASN][1000 genomes]
rs74140973	0.90[ASN][1000 genomes]
rs74140976	0.90[ASN][1000 genomes]
rs74140978	0.90[ASN][1000 genomes]
rs74140980	0.90[ASN][1000 genomes]
rs74140989	0.90[ASN][1000 genomes]
rs74140994	0.90[ASN][1000 genomes]
rs74140996	0.90[ASN][1000 genomes]
rs74141002	0.90[ASN][1000 genomes]
rs74142606	0.90[ASN][1000 genomes]
rs74142608	0.90[ASN][1000 genomes]
rs74142625	0.90[ASN][1000 genomes]
rs74142627	0.90[ASN][1000 genomes]
rs74142642	0.90[ASN][1000 genomes]
rs74142644	0.90[ASN][1000 genomes]
rs74142645	0.90[ASN][1000 genomes]
rs74142647	0.90[ASN][1000 genomes]
rs74143623	1.00[AFR][1000 genomes]
rs74143631	1.00[ASN][1000 genomes]
rs74143632	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74143634	1.00[ASN][1000 genomes]
rs74143635	1.00[ASN][1000 genomes]
rs74143636	1.00[ASN][1000 genomes]
rs74143637	1.00[ASN][1000 genomes]
rs74143638	1.00[ASN][1000 genomes]
rs74143640	1.00[ASN][1000 genomes]
rs74143641	1.00[ASN][1000 genomes]
rs74143642	1.00[ASN][1000 genomes]
rs74143662	1.00[ASN][1000 genomes]
rs74143663	1.00[AFR][1000 genomes]
rs74143665	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74143667	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs752108	1.00[ASN][1000 genomes]
rs752109	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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228271600-228278600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr1:228272400-228279400	Genic enhancers	Fetal Muscle Leg	muscle
3	chr1:228272400-228280000	Genic enhancers	Fetal Thymus	thymus
4	chr1:228272400-228284400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:228272600-228278400	Enhancers	Small Intestine	intestine
6	chr1:228272600-228280200	Enhancers	Fetal Heart	heart
7	chr1:228272800-228278600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:228272800-228278600	Genic enhancers	Fetal Stomach	stomach
9	chr1:228273000-228277400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:228273000-228279200	Genic enhancers	Fetal Intestine Small	intestine
11	chr1:228273000-228284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:228273400-228277600	Enhancers	Brain Cingulate Gyrus	brain
13	chr1:228273400-228278200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:228273400-228279000	Genic enhancers	HepG2	liver
15	chr1:228273400-228280200	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr1:228273400-228285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr1:228273600-228277200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:228273600-228277400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:228273600-228277800	Genic enhancers	Dnd41	blood
20	chr1:228273600-228278200	Weak transcription	Fetal Brain Male	brain
21	chr1:228273600-228278200	Genic enhancers	K562	blood
22	chr1:228273600-228281800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:228273800-228279200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:228274000-228279200	Enhancers	Colon Smooth Muscle	Colon
25	chr1:228274000-228280600	Enhancers	Psoas Muscle	Psoas
26	chr1:228274200-228281200	Genic enhancers	Liver	Liver
27	chr1:228274600-228277200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
28	chr1:228274600-228278200	Genic enhancers	A549	lung
29	chr1:228274600-228278800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:228274600-228278800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:228274600-228280600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:228274800-228277400	Genic enhancers	Rectal Mucosa Donor 29	rectum
33	chr1:228274800-228278800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
34	chr1:228274800-228279200	Genic enhancers	Fetal Intestine Large	intestine
35	chr1:228275000-228277200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:228275200-228276800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr1:228275200-228276800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:228275200-228280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:228275200-228282000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:228275400-228277200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:228275400-228277600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:228275400-228278200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:228275400-228279200	Genic enhancers	Fetal Muscle Trunk	muscle
44	chr1:228275400-228281200	Genic enhancers	Gastric	stomach
45	chr1:228275400-228281400	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr1:228275600-228277600	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr1:228275600-228277800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:228275600-228277800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:228275600-228278200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
50	chr1:228275600-228279200	Genic enhancers	Thymus	Thymus

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