Variant report

Variant	rs6541388
Chromosome Location	chr1:94148133-94148134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94147920-94148175	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr1:94148098-94148204	A549	lung:	n/a	chr1:94148158-94148169
3	POLR2A	chr1:94145532-94148138	HUVEC	blood vessel:	n/a	n/a
4	CEBPB	chr1:94147986-94148286	K562	blood:	n/a	chr1:94148158-94148169
5	CEBPB	chr1:94148115-94148216	H1-hESC	embryonic stem cell:	n/a	chr1:94148158-94148169
6	CEBPB	chr1:94148068-94148295	Hela-S3	cervix:	n/a	chr1:94148158-94148169
7	CTCF	chr1:94146996-94148138	A549	lung:	n/a	chr1:94147374-94147387 chr1:94147374-94147387 chr1:94147846-94147854
8	RAD21	chr1:94145132-94148255	SK-N-SH	brain:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
9	CEBPB	chr1:94148016-94148308	IMR90	lung:	n/a	chr1:94148158-94148169

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:94148127-94148177	AoSMC	blood vessel:	n/a
2	chr1:94148127-94148177	NH-A	brain:	n/a
3	chr1:94148127-94148177	BJ	skin:	n/a
4	chr1:94148127-94148177	T-47D	breast:	n/a
5	chr1:94148127-94148177	H1-hESC	embryonic stem cell:	embryo
6	chr1:94148127-94148177	ovcar-3	ovarian:	n/a
7	chr1:94148127-94148177	HRE	kidney:	n/a
8	chr1:94148127-94148177	AG09309	skin:	n/a
9	chr1:94148127-94148177	Hela-S3	cervix:	n/a
10	chr1:94148127-94148177	U87	brain:	n/a
11	chr1:94148127-94148177	MCF-7	breast:	n/a
12	chr1:94148127-94148177	GM19239	blood:	n/a
13	chr1:94148127-94148177	HCT-116	colon:	n/a
14	chr1:94148127-94148177	ProgFib	skin:	n/a
15	chr1:94148127-94148177	HRCEpiC	kidney:	n/a
16	chr1:94148127-94148177	LNCaP	prostate:	n/a
17	chr1:94148127-94148177	NHBE	bronchial:	n/a
18	chr1:94148127-94148177	MCF10A-Er-Src	breast:	n/a
19	chr1:94148127-94148177	A549	lung:	n/a
20	chr1:94148127-94148177	AG10803	skin:	n/a
21	chr1:94148127-94148177	ECC-1	luminal epithelium:	n/a
22	chr1:94148127-94148177	GM06990	blood:	n/a
23	chr1:94148127-94148177	HMEC	breast:	n/a
24	chr1:94148127-94148177	SKMC	muscle:	n/a
25	chr1:94148127-94148177	RPTEC	kidney:	n/a
26	chr1:94148127-94148177	CMK	blood:	n/a
27	chr1:94148127-94148177	HL-60	blood:	n/a
28	chr1:94148127-94148177	HUVEC	blood vessel:	n/a
29	chr1:94148127-94148177	SK-N-SH_RA	brain:	n/a
30	chr1:94148127-94148177	BE2_C	brain:	n/a
31	chr1:94148127-94148177	AG09319	gingival:	n/a
32	chr1:94148127-94148177	GM12892	blood:	n/a
33	chr1:94148127-94148177	GM12878	blood:	n/a
34	chr1:94148127-94148177	HIPEpiC	eye:	n/a
35	chr1:94148127-94148177	K562	blood:	n/a
36	chr1:94148127-94148177	NT2-D1	testis:	n/a
37	chr1:94148127-94148177	Caco-2	colon:	n/a
38	chr1:94148127-94148177	HAEpiC	amniotic membrane:	n/a
39	chr1:94148127-94148177	HepG2	liver:	n/a
40	chr1:94148127-94148177	Jurkat	blood:	n/a
41	chr1:94148127-94148177	HPAEpiC	pulmonary alveolar:	n/a
42	chr1:94148127-94148177	HEEpiC	esophagus:	n/a
43	chr1:94148127-94148177	HNPCEpiC	eye:	n/a
44	chr1:94148127-94148177	SAEC	small airway:	n/a
45	chr1:94148127-94148177	HRPEpiC	eye:	n/a
46	chr1:94148127-94148177	HEK293	kidney:	embryo
47	chr1:94148127-94148177	AG04449	skin:	fetal
48	chr1:94148127-94148177	NB4	blood:	n/a
49	chr1:94148127-94148177	IMR90	lung:	fetal
50	chr1:94148127-94148177	PrEC	prostate:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:93913059..93915471-chr1:94146480..94149352,2	MCF-7	breast:
2	chr1:94145898..94148493-chr1:94311257..94313086,3	MCF-7	breast:
3	chr1:94147624..94149289-chr1:94160364..94162854,2	MCF-7	breast:

No data

Variant related genes	Relation type
BCAR3	TF binding region
BCAR3	CpG island
ENSG00000260464	Chromatin interaction
ENSG00000137942	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000211575	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011903	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164962	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164963	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057736	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12079723	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12084853	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12092517	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1567791	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781002	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541386	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6656270	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6657709	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6660740	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701871	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6702036	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704479	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7519952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs955470	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9659100	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94144400-94148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:94144600-94148400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:94145400-94148400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:94145400-94148400	Active TSS	HSMM	muscle
5	chr1:94145600-94148200	Active TSS	A549	lung
6	chr1:94145800-94148200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:94146000-94148200	Active TSS	Brain Angular Gyrus	brain
8	chr1:94147400-94148200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr1:94147600-94148200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
10	chr1:94147600-94148200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:94147600-94148200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:94147600-94148200	Flanking Active TSS	Hela-S3	cervix
13	chr1:94147600-94148200	Flanking Active TSS	NHEK	skin
14	chr1:94147600-94148200	Flanking Active TSS	Osteobl	bone
15	chr1:94147800-94148200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:94147800-94148200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
17	chr1:94147800-94148200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:94147800-94148200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:94147800-94148200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
20	chr1:94147800-94148200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:94147800-94148200	Enhancers	Brain Substantia Nigra	brain
22	chr1:94147800-94148200	Flanking Active TSS	Colonic Mucosa	Colon
23	chr1:94147800-94148200	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr1:94147800-94148200	Enhancers	Lung	lung
25	chr1:94147800-94148200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:94147800-94148200	Flanking Active TSS	HMEC	breast
27	chr1:94147800-94148200	Flanking Active TSS	NHDF-Ad	bronchial
28	chr1:94147800-94148400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:94147800-94153200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:94148000-94148200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
31	chr1:94148000-94148200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:94148000-94148200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:94148000-94148200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:94148000-94148200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:94148000-94148200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
36	chr1:94148000-94148200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:94148000-94148200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:94148000-94148200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:94148000-94148200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:94148000-94148200	Enhancers	Primary B cells from cord blood	blood
41	chr1:94148000-94148200	Enhancers	Primary B cells from peripheral blood	blood
42	chr1:94148000-94148200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr1:94148000-94148200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:94148000-94148200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:94148000-94148200	Enhancers	Brain Cingulate Gyrus	brain
46	chr1:94148000-94148200	Enhancers	Brain Hippocampus Middle	brain
47	chr1:94148000-94148200	Enhancers	Colon Smooth Muscle	Colon
48	chr1:94148000-94148200	Active TSS	Duodenum Mucosa	Duodenum
49	chr1:94148000-94148200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:94148000-94148200	Enhancers	Fetal Intestine Small	intestine

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