Variant report

Variant	rs28381462
Chromosome Location	chr6:88300232-88300233
allele	A/G/T
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	RUNX3	chr6:88299386-88300272	GM12878	blood:	n/a	n/a
2	RUNX3	chr6:88299337-88300299	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:88299252-88300238	GM12892	blood:	n/a	n/a
4	ZNF143	chr6:88299487-88300318	H1-hESC	embryonic stem cell:	n/a	n/a
5	GABPA	chr6:88299060-88300322	A549	lung:	n/a	n/a
6	ELF1	chr6:88299396-88300250	MCF-7	breast:	n/a	n/a
7	PAX5	chr6:88299511-88300262	GM12878	blood:	n/a	chr6:88299831-88299840
8	POLR2A	chr6:88299330-88300255	NB4	blood:	n/a	n/a
9	BHLHE40	chr6:88299176-88300272	K562	blood:	n/a	chr6:88299823-88299839
10	POLR2A	chr6:88298921-88300389	HepG2	liver:	n/a	n/a
11	PML	chr6:88299360-88300242	K562	blood:	n/a	n/a
12	SMC3	chr6:88299471-88300243	Hela-S3	cervix:	n/a	n/a
13	USF2	chr6:88299556-88300267	H1-hESC	embryonic stem cell:	n/a	chr6:88299823-88299839
14	RCOR1	chr6:88299195-88300503	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:88299333-88300350	HL-60	blood:	n/a	n/a
16	POLR2A	chr6:88299102-88300725	HepG2	liver:	n/a	n/a
17	MAX	chr6:88299322-88300359	A549	lung:	n/a	n/a
18	REST	chr6:88299328-88300287	HL-60	blood:	n/a	n/a
19	TEAD4	chr6:88299735-88300245	H1-hESC	embryonic stem cell:	n/a	n/a
20	TBP	chr6:88299270-88300279	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr6:88299295-88300271	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr6:88299395-88300329	K562	blood:	n/a	n/a
23	GABPA	chr6:88299246-88300373	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr6:88299345-88300235	MCF-7	breast:	n/a	n/a
25	POLR2A	chr6:88299379-88300274	H1-neurons	neurons:	n/a	n/a
26	NR2F2	chr6:88299258-88300509	K562	blood:	n/a	chr6:88299811-88299826
27	GABPA	chr6:88299019-88300460	MCF-7	breast:	n/a	n/a
28	POLR2A	chr6:88299349-88300253	Gliobla	brain:	n/a	n/a
29	MAX	chr6:88299235-88300293	MCF-7	breast:	n/a	n/a
30	GABPA	chr6:88299240-88300310	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr6:88299319-88300300	H1-hESC	embryonic stem cell:	n/a	n/a
32	SIN3AK20	chr6:88299143-88300446	MCF-7	breast:	n/a	n/a
33	KAP1	chr6:88299090-88300327	HEK293	kidney:	n/a	n/a
34	CREB1	chr6:88299512-88300252	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr6:88299241-88300286	Hela-S3	cervix:	n/a	n/a
36	MAX	chr6:88299489-88300308	H1-hESC	embryonic stem cell:	n/a	n/a
37	E2F4	chr6:88299204-88300993	MCF10A-Er-Src	breast:	n/a	chr6:88299841-88299848 chr6:88299841-88299848 chr6:88299838-88299849 chr6:88299837-88299849 chr6:88299781-88299790 chr6:88299841-88299848
38	RELA	chr6:88299408-88300252	GM18505	blood:	n/a	chr6:88299844-88299853 chr6:88299844-88299853
39	FOXM1	chr6:88299325-88300312	GM12878	blood:	n/a	n/a
40	CHD2	chr6:88299329-88300298	GM12878	blood:	n/a	chr6:88299745-88299755 chr6:88299715-88299725
41	MAX	chr6:88299402-88300293	SK-N-SH	brain:	n/a	n/a
42	MAX	chr6:88299427-88300266	ECC-1	luminal epithelium:	n/a	n/a
43	POLR2A	chr6:88299397-88300251	H1-hESC	embryonic stem cell:	n/a	n/a
44	TAF1	chr6:88299268-88300371	H1-hESC	embryonic stem cell:	n/a	n/a
45	PML	chr6:88299089-88300288	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:88299255-88300332	SK-N-MC	brain:	n/a	n/a
47	POLR2A	chr6:88299423-88300359	K562	blood:	n/a	n/a
48	RCOR1	chr6:88299203-88300315	K562	blood:	n/a	n/a
49	YY1	chr6:88299383-88300245	H1-hESC	embryonic stem cell:	n/a	n/a
50	RCOR1	chr6:88299392-88300247	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:88298942..88303064-chr6:88409165..88412231,4	K562	blood:
2	chr6:88299673..88301546-chr6:89673147..89674942,2	K562	blood:
3	chr6:88299988..88301682-chr6:88305873..88308812,2	K562	blood:
4	chr1:117602497..117603240-chr6:88299651..88300387,2	Hela-S3	cervix:
5	chr6:88299553..88301559-chr6:88410382..88412634,2	MCF-7	breast:
6	chr20:18547409..18548100-chr6:88299330..88300266,2	NB4	blood:
7	chr6:88299642..88300403-chrX:47076850..47077430,2	Hela-S3	cervix:
8	chr6:88181710..88183852-chr6:88298759..88301128,2	K562	blood:
9	chr6:88299715..88302499-chr6:88315597..88317409,2	MCF-7	breast:
10	chr6:88277452..88280023-chr6:88298199..88301235,3	MCF-7	breast:

Variant related genes	Relation type
RARS2	TF binding region
ENSG00000111880	Chromatin interaction
ENSG00000135336	Chromatin interaction
ENSG00000232388	Chromatin interaction
ENSG00000146282	Chromatin interaction
ENSG00000135334	Chromatin interaction
ENSG00000203863	Chromatin interaction
ENSG00000116830	Chromatin interaction
ENSG00000102225	Chromatin interaction
ENSG00000164414	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13347346	1.00[AMR][1000 genomes]
rs2092646	1.00[AMR][1000 genomes]
rs73752045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88297800-88301200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:88297800-88301400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr6:88298000-88300600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:88298000-88300800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:88298000-88301000	Active TSS	HSMM	muscle
6	chr6:88298000-88301400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:88298000-88301400	Active TSS	A549	lung
8	chr6:88298200-88300600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:88298200-88300600	Active TSS	Colonic Mucosa	Colon
10	chr6:88298200-88300800	Active TSS	Fetal Intestine Large	intestine
11	chr6:88298200-88301000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:88298200-88301000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:88298200-88301200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:88298400-88300400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:88298400-88300600	Active TSS	Fetal Stomach	stomach
16	chr6:88298400-88300600	Active TSS	Lung	lung
17	chr6:88298400-88300800	Active TSS	Fetal Muscle Trunk	muscle
18	chr6:88298400-88300800	Active TSS	Right Atrium	heart
19	chr6:88298400-88300800	Active TSS	HSMMtube	muscle
20	chr6:88298400-88301000	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr6:88298600-88300600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:88298600-88300600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:88298600-88300600	Active TSS	Ovary	ovary
24	chr6:88298600-88300600	Active TSS	Pancreas	Pancrea
25	chr6:88298600-88300600	Active TSS	HMEC	breast
26	chr6:88298600-88300600	Active TSS	K562	blood
27	chr6:88298600-88300600	Active TSS	NHLF	lung
28	chr6:88298600-88300800	Active TSS	Aorta	Aorta
29	chr6:88298600-88300800	Active TSS	Left Ventricle	heart
30	chr6:88298600-88300800	Active TSS	Psoas Muscle	Psoas
31	chr6:88298600-88301000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr6:88298600-88301000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:88298800-88300400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:88298800-88300400	Active TSS	Brain Anterior Caudate	brain
35	chr6:88298800-88300400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr6:88298800-88300400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr6:88298800-88300400	Active TSS	Fetal Lung	lung
38	chr6:88298800-88300400	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr6:88298800-88300400	Active TSS	Stomach Mucosa	stomach
40	chr6:88298800-88300400	Active TSS	HUVEC	blood vessel
41	chr6:88298800-88300400	Active TSS	NH-A	brain
42	chr6:88298800-88300400	Active TSS	Osteobl	bone
43	chr6:88298800-88300600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:88298800-88300600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:88298800-88300600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:88298800-88300600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:88298800-88300600	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr6:88298800-88300600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:88298800-88300600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:88298800-88300600	Active TSS	Colon Smooth Muscle	Colon

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