Variant report

Variant	rs58040059
Chromosome Location	chr6:27780659-27780660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27780645-27780925	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:27779808-27783925	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr6:27779782-27781254	H1-hESC	embryonic stem cell:	n/a	n/a
4	HEY1	chr6:27780347-27780949	K562	blood:	n/a	n/a
5	CCNT2	chr6:27780388-27780994	K562	blood:	n/a	n/a
6	STAT5A	chr6:27780619-27781272	K562	blood:	n/a	n/a
7	PML	chr6:27776216-27781822	K562	blood:	n/a	chr6:27777813-27777821
8	POLR2A	chr6:27779867-27781271	K562	blood:	n/a	n/a
9	MEF2A	chr6:27780390-27781262	K562	blood:	n/a	chr6:27780979-27780993 chr6:27780978-27780994 chr6:27780979-27780994 chr6:27780962-27780970 chr6:27780974-27780995
10	ATF2	chr6:27780520-27782252	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:27779792-27781213	K562	blood:	n/a	n/a
12	POLR2A	chr6:27776207-27781903	K562	blood:	n/a	n/a
13	TAF7	chr6:27776220-27782251	H1-hESC	embryonic stem cell:	n/a	n/a
14	ETS1	chr6:27780577-27780876	K562	blood:	n/a	n/a
15	POLR2A	chr6:27774157-27784396	MCF-7	breast:	n/a	n/a
16	TEAD4	chr6:27776216-27781908	K562	blood:	n/a	n/a
17	TAF1	chr6:27780629-27780998	K562	blood:	n/a	n/a
18	POLR2A	chr6:27780641-27780875	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr6:27776241-27781173	K562	blood:	n/a	n/a
20	POLR2A	chr6:27779797-27781018	K562	blood:	n/a	n/a
21	SIN3AK20	chr6:27780442-27781419	K562	blood:	n/a	n/a
22	IRF1	chr6:27780535-27780714	K562	blood:	n/a	n/a
23	HEY1	chr6:27779767-27781180	K562	blood:	n/a	n/a
24	POLR2A	chr6:27780535-27780927	H1-hESC	embryonic stem cell:	n/a	n/a
25	NR2F2	chr6:27780299-27781289	K562	blood:	n/a	n/a
26	MAX	chr6:27780550-27781010	K562	blood:	n/a	n/a
27	CHD2	chr6:27780637-27780781	K562	blood:	n/a	n/a
28	TBL1XR1	chr6:27780600-27781085	K562	blood:	n/a	n/a
29	POLR2A	chr6:27780326-27784278	PANC-1	pancreas:	n/a	n/a
30	CEBPD	chr6:27780397-27781735	K562	blood:	n/a	n/a
31	BCLAF1	chr6:27779724-27781893	K562	blood:	n/a	n/a
32	CBX3	chr6:27780469-27781263	K562	blood:	n/a	n/a
33	POLR2A	chr6:27780152-27784269	PANC-1	pancreas:	n/a	n/a
34	POLR2A	chr6:27776242-27782187	K562	blood:	n/a	n/a
35	NFIC	chr6:27780650-27783972	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:27780640-27780828	Hela-S3	cervix:	n/a	n/a
37	UBTF	chr6:27780423-27780990	K562	blood:	n/a	n/a
38	FOSL1	chr6:27780596-27780969	K562	blood:	n/a	n/a
39	POLR2A	chr6:27773907-27784120	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr6:27779891-27784007	PBDE	blood:	n/a	n/a
41	CHD1	chr6:27774579-27782547	H1-hESC	embryonic stem cell:	n/a	chr6:27775204-27775214 chr6:27778702-27778712
42	POLR2A	chr6:27779814-27783780	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:27775490-27781797	K562	blood:	n/a	n/a
44	BCLAF1	chr6:27780244-27781151	K562	blood:	n/a	n/a
45	POLR2A	chr6:27780653-27780851	ProgFib	skin:	n/a	n/a
46	POLR2A	chr6:27780528-27784231	GM12878	blood:	n/a	n/a

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26122455..26127911-chr6:27777953..27784057,9	MCF-7	breast:
2	chr5:137802010..137804655-chr6:27778426..27781380,2	K562	blood:
3	chr6:27173443..27175541-chr6:27778725..27781351,2	K562	blood:
4	chr6:27121049..27122918-chr6:27780624..27782591,2	K562	blood:
5	chr6:27780572..27782800-chr6:28000600..28002491,2	K562	blood:
6	chr6:27093369..27111594-chr6:27770152..27782376,64	K562	blood:
7	chr6:27780093..27783062-chr6:28322537..28324933,2	K562	blood:
8	chr6:26033235..26035308-chr6:27778375..27781238,2	MCF-7	breast:
9	chr22:39639283..39641253-chr6:27780476..27782523,2	MCF-7	breast:
10	chr6:27779510..27781732-chr6:28104870..28106690,2	K562	blood:
11	chr6:27778740..27781268-chr6:30683487..30686226,2	K562	blood:
12	chr6:27735339..27736956-chr6:27780482..27782528,2	MCF-7	breast:
13	chr6:26215420..26218815-chr6:27778137..27782519,4	MCF-7	breast:
14	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
15	chr6:27779050..27781755-chr6:28103031..28104802,2	K562	blood:
16	chr17:57105669..57107774-chr6:27778855..27781686,2	MCF-7	breast:
17	chr14:50360748..50362571-chr6:27780404..27782536,2	MCF-7	breast:
18	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
19	chr6:26275391..26278113-chr6:27778905..27781292,2	MCF-7	breast:
20	chr6:26214475..26216375-chr6:27779418..27781411,2	K562	blood:
21	chr6:26025862..26028751-chr6:27778385..27781122,2	MCF-7	breast:
22	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
23	chr6:26286125..26287830-chr6:27780556..27782142,2	K562	blood:
24	chr6:27775597..27780846-chr6:28300467..28304976,7	K562	blood:
25	chr21:40407439..40410203-chr6:27778670..27781408,2	MCF-7	breast:
26	chr6:26029300..26031904-chr6:27779187..27780986,2	K562	blood:
27	chr6:27518639..27521498-chr6:27778464..27780715,2	K562	blood:
28	chr11:59313285..59315331-chr6:27779398..27781335,2	K562	blood:
29	chr6:26020260..26024010-chr6:27780504..27784636,5	MCF-7	breast:
30	chr6:27104887..27109324-chr6:27780147..27783327,4	MCF-7	breast:
31	chr6:26054474..26058085-chr6:27777303..27780745,6	MCF-7	breast:
32	chr6:26188383..26190588-chr6:27780169..27782102,2	MCF-7	breast:
33	chr6:26198117..26201141-chr6:27779644..27782076,3	MCF-7	breast:
34	chr6:27111749..27120986-chr6:27774460..27781468,38	K562	blood:

No data

Variant related genes	Relation type
HIST1H2BM	TF binding region
HIST1H2BL	TF binding region
ENSG00000196176	Chromatin interaction
ENSG00000100311	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000217315	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000180596	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs55761446	1.00[AMR][1000 genomes]
rs55810724	1.00[AMR][1000 genomes]
rs56096322	1.00[AMR][1000 genomes]
rs56358872	1.00[AMR][1000 genomes]
rs56393640	1.00[AMR][1000 genomes]
rs57044733	1.00[AMR][1000 genomes]
rs57270702	1.00[AMR][1000 genomes]
rs57606279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58677321	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60242525	1.00[AMR][1000 genomes]
rs60512267	1.00[AMR][1000 genomes]
rs60542036	1.00[AMR][1000 genomes]
rs60566574	1.00[AMR][1000 genomes]
rs61499563	1.00[AMR][1000 genomes]
rs73739605	1.00[AMR][1000 genomes]
rs73739607	1.00[AMR][1000 genomes]
rs73739608	1.00[AMR][1000 genomes]
rs73739609	1.00[AMR][1000 genomes]
rs73739686	1.00[AMR][1000 genomes]
rs73739687	1.00[AMR][1000 genomes]
rs73739689	1.00[AMR][1000 genomes]
rs73739691	1.00[AMR][1000 genomes]
rs73739696	1.00[AMR][1000 genomes]
rs73740807	1.00[AMR][1000 genomes]
rs73740808	1.00[AMR][1000 genomes]
rs73740809	1.00[AMR][1000 genomes]
rs73740816	1.00[AMR][1000 genomes]
rs73740819	1.00[AMR][1000 genomes]
rs73740835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73740839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73740841	0.93[AFR][1000 genomes]
rs73740871	1.00[AMR][1000 genomes]
rs73740872	1.00[AMR][1000 genomes]
rs73740874	1.00[AMR][1000 genomes]
rs73740882	1.00[AMR][1000 genomes]
rs73741616	1.00[AMR][1000 genomes]
rs73741620	1.00[AMR][1000 genomes]
rs73741622	1.00[AMR][1000 genomes]
rs73741623	1.00[AMR][1000 genomes]
rs9767465	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27774400-27784000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:27778000-27782200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:27778200-27782400	Weak transcription	Spleen	Spleen
4	chr6:27778400-27781800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:27778400-27782400	Weak transcription	Lung	lung
6	chr6:27778400-27782400	Weak transcription	Pancreas	Pancrea
7	chr6:27778600-27782600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:27778800-27781600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:27778800-27782000	Weak transcription	Placenta	Placenta
10	chr6:27779000-27781600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:27779000-27781600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:27779000-27781600	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:27779000-27781800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:27779000-27781800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:27779000-27782000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:27779000-27782000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:27779000-27782000	Weak transcription	Fetal Brain Male	brain
18	chr6:27779000-27782000	Weak transcription	HSMMtube	muscle
19	chr6:27779000-27782400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:27779200-27781400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:27779200-27781800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:27779200-27782000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:27779400-27781000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:27779400-27781000	Weak transcription	HMEC	breast
25	chr6:27779400-27781200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:27779400-27781200	Weak transcription	NHEK	skin
27	chr6:27779400-27781400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:27779400-27781400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr6:27779400-27781400	Weak transcription	HUVEC	blood vessel
30	chr6:27779400-27781600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:27779400-27781600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:27779400-27781600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:27779400-27781600	Weak transcription	Fetal Brain Female	brain
34	chr6:27779400-27781600	Weak transcription	Fetal Stomach	stomach
35	chr6:27779400-27781600	Weak transcription	NHLF	lung
36	chr6:27779400-27781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:27779400-27781800	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:27779400-27781800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr6:27779400-27781800	Weak transcription	Liver	Liver
40	chr6:27779400-27781800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:27779400-27781800	Weak transcription	HSMM	muscle
42	chr6:27779400-27781800	Weak transcription	Osteobl	bone
43	chr6:27779400-27782000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:27779400-27782000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:27779400-27782000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:27779400-27782000	Weak transcription	Fetal Lung	lung
47	chr6:27779400-27782400	Weak transcription	Stomach Mucosa	stomach
48	chr6:27779600-27780800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:27779600-27780800	Enhancers	Primary B cells from cord blood	blood
50	chr6:27779600-27781000	Weak transcription	Fetal Kidney	kidney

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