Variant report

Variant	rs2147959
Chromosome Location	chr1:228644232-228644233
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228643988-228647458	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:228644064-228646619	MCF10A-Er-Src	breast:	n/a	n/a
3	ELK1	chr1:228643322-228644577	K562	blood:	n/a	n/a
4	HEY1	chr1:228643995-228644420	K562	blood:	n/a	n/a
5	POLR2A	chr1:228643891-228645953	K562	blood:	n/a	n/a
6	IRF1	chr1:228644053-228646533	K562	blood:	n/a	chr1:228644336-228644353 chr1:228645651-228645660 chr1:228645551-228645563 chr1:228645551-228645568 chr1:228644543-228644550
7	ZNF274	chr1:228643104-228644282	K562	blood:	n/a	n/a
8	MXI1	chr1:228643446-228645971	K562	blood:	n/a	n/a
9	POLR2A	chr1:228644034-228646552	K562	blood:	n/a	n/a
10	POLR2A	chr1:228644071-228644263	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr1:228644231-228644371	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:228639970-228646628	K562	blood:	n/a	n/a
13	CTCF	chr1:228644100-228644250	HPAF	blood vessel:	n/a	n/a
14	POLR2A	chr1:228644075-228647651	GM12891	blood:	n/a	n/a
15	MAFF	chr1:228644081-228644752	K562	blood:	n/a	n/a
16	POLR2A	chr1:228642791-228644400	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr1:228642891-228647849	SK-N-SH	brain:	n/a	n/a
18	BCLAF1	chr1:228643516-228646002	K562	blood:	n/a	n/a
19	POLR2A	chr1:228643224-228647569	PBDE	blood:	n/a	n/a
20	BCLAF1	chr1:228642976-228646006	K562	blood:	n/a	n/a

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228643230..228649256-chr1:228671672..228678578,15	MCF-7	breast:
2	chr1:228643588..228645141-chr12:57117771..57120124,2	K562	blood:
3	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
4	chr1:228644193..228646500-chr17:56735142..56738060,2	MCF-7	breast:
5	chr1:228589639..228603795-chr1:228638211..228648676,43	MCF-7	breast:
6	chr1:228400987..228403639-chr1:228644070..228647036,3	K562	blood:
7	chr1:228356236..228360236-chr1:228642827..228646319,4	K562	blood:
8	chr1:228635196..228636992-chr1:228643144..228645156,2	MCF-7	breast:
9	chr1:228527319..228529174-chr1:228643388..228645419,2	K562	blood:
10	chr1:228579742..228582257-chr1:228643966..228647332,3	MCF-7	breast:
11	chr1:228576966..228583255-chr1:228642395..228646960,7	MCF-7	breast:
12	chr1:228629848..228632081-chr1:228641803..228644733,3	MCF-7	breast:
13	chr1:228585219..228604537-chr1:228641966..228650471,45	MCF-7	breast:
14	chr1:228540366..228544195-chr1:228644232..228647722,5	K562	blood:
15	chr1:228326283..228328223-chr1:228644101..228647229,3	K562	blood:
16	chr1:228487421..228490284-chr1:228642945..228645518,2	K562	blood:
17	chr1:228644136..228646593-chr1:229642756..229644916,2	K562	blood:
18	chr1:228572036..228574709-chr1:228642846..228645272,2	K562	blood:
19	chr1:228461911..228467066-chr1:228644143..228647181,7	K562	blood:
20	chr1:228352175..228354992-chr1:228642370..228645679,3	K562	blood:
21	chr1:228110564..228113344-chr1:228642639..228644578,2	K562	blood:
22	chr1:226111842..226114398-chr1:228644051..228646541,2	K562	blood:
23	chr1:228295701..228298276-chr1:228642852..228645061,2	K562	blood:
24	chr1:228357413..228360288-chr1:228642904..228645646,2	K562	blood:
25	chr1:228269292..228271024-chr1:228643891..228647144,3	K562	blood:
26	chr1:228351867..228354707-chr1:228644066..228646838,3	K562	blood:
27	chr1:228290061..228293195-chr1:228643504..228645569,3	K562	blood:
28	chr1:228271974..228275319-chr1:228643789..228645457,3	K562	blood:
29	chr1:228643550..228646999-chr1:228697754..228701028,5	K562	blood:
30	chr1:228272480..228275319-chr1:228642509..228645344,2	K562	blood:
31	chr1:228644058..228645584-chr20:49575003..49577422,2	MCF-7	breast:
32	chr1:228270437..228272083-chr1:228644163..228645827,2	MCF-7	breast:
33	chr1:228642342..228647806-chr1:228672380..228678428,13	MCF-7	breast:
34	chr1:228326723..228329419-chr1:228644101..228647035,3	K562	blood:
35	chr1:228461911..228467066-chr1:228644125..228647181,7	K562	blood:
36	chr1:228327593..228329181-chr1:228644179..228646860,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIST3H2BB	TF binding region
ENSG00000143761	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000269890	Chromatin interaction
ENSG00000000419	Chromatin interaction
ENSG00000124217	Chromatin interaction
ENSG00000270104	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000143811	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000162931	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000069248	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000162913	Chromatin interaction
ENSG00000168159	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000215811	Chromatin interaction
ENSG00000196531	Chromatin interaction
ENSG00000270094	Chromatin interaction
ENSG00000231563	Chromatin interaction
ENSG00000223635	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1007686	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10916313	0.94[EUR][1000 genomes]
rs10916314	0.89[EUR][1000 genomes]
rs10916317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587839	0.94[EUR][1000 genomes]
rs12131962	0.89[EUR][1000 genomes]
rs12725863	0.95[EUR][1000 genomes]
rs1886774	0.87[EUR][1000 genomes]
rs4653551	0.94[EUR][1000 genomes]
rs4653552	0.94[EUR][1000 genomes]
rs4653960	0.94[EUR][1000 genomes]
rs6426503	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6659690	0.94[EUR][1000 genomes]
rs6666241	0.94[EUR][1000 genomes]
rs7524236	0.95[EUR][1000 genomes]
rs7529055	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7533319	0.83[ASN][1000 genomes]
rs7555298	0.89[EUR][1000 genomes]
rs7555386	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
9	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
10	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
12	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
14	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228634200-228644800	Weak transcription	Gastric	stomach
2	chr1:228634400-228644600	Weak transcription	Right Atrium	heart
3	chr1:228634400-228644600	Weak transcription	Right Ventricle	heart
4	chr1:228638400-228644600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:228638800-228644600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:228640400-228644800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:228640600-228644800	Weak transcription	Esophagus	oesophagus
8	chr1:228641000-228644600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:228641000-228644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:228641800-228644800	Weak transcription	Spleen	Spleen
11	chr1:228642200-228644400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:228642200-228644800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:228642800-228644600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:228643000-228644400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:228643000-228644400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr1:228643000-228644400	Flanking Active TSS	Fetal Brain Female	brain
17	chr1:228643000-228644600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:228643000-228647800	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:228643000-228648200	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr1:228643200-228644600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:228643200-228644600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:228643200-228647600	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr1:228643200-228647600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:228643200-228647800	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:228643200-228647800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:228643200-228647800	Active TSS	A549	lung
27	chr1:228643400-228644400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr1:228643400-228644600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr1:228643400-228644600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:228643400-228644600	Enhancers	Fetal Heart	heart
31	chr1:228643400-228644800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:228643400-228644800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:228643400-228644800	Active TSS	Brain Hippocampus Middle	brain
34	chr1:228643400-228644800	Active TSS	Placenta	Placenta
35	chr1:228643400-228646000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:228643400-228646000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:228643400-228647200	Active TSS	Hela-S3	cervix
38	chr1:228643400-228647400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr1:228643400-228647400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:228643400-228647400	Active TSS	GM12878-XiMat	blood
41	chr1:228643400-228647600	Active TSS	H9 Cell Line	embryonic stem cell
42	chr1:228643400-228647800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr1:228643400-228647800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr1:228643400-228647800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:228643600-228645600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:228643600-228647000	Active TSS	Brain Angular Gyrus	brain
47	chr1:228643800-228644400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:228643800-228644600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:228643800-228644800	Active TSS	Brain Germinal Matrix	brain
50	chr1:228643800-228645000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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