Variant report

Variant	rs541154
Chromosome Location	chr8:102504541-102504542
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:104)
CpG islands
(count:61)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:104 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr8:102504121-102505124	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr8:102504400-102505243	ECC-1	luminal epithelium:	n/a	n/a
3	MXI1	chr8:102503778-102505103	H1-hESC	embryonic stem cell:	n/a	chr8:102504017-102504026
4	MAX	chr8:102504236-102505086	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr8:102504484-102505106	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3AK20	chr8:102503452-102505487	MCF-7	breast:	n/a	n/a
7	POLR2A	chr8:102502831-102507688	MCF-7	breast:	n/a	n/a
8	YY1	chr8:102504129-102505121	HCT-116	colon:	n/a	n/a
9	MAX	chr8:102503808-102506777	MCF-7	breast:	n/a	chr8:102506109-102506119
10	CHD1	chr8:102503893-102505526	H1-hESC	embryonic stem cell:	n/a	n/a
11	PML	chr8:102503675-102506920	MCF-7	breast:	n/a	n/a
12	TAF7	chr8:102504293-102505017	H1-hESC	embryonic stem cell:	n/a	n/a
13	E2F6	chr8:102504226-102505000	H1-hESC	embryonic stem cell:	n/a	chr8:102504601-102504610
14	CTBP2	chr8:102503748-102505001	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr8:102504017-102506789	HCT-116	colon:	n/a	n/a
16	SIN3AK20	chr8:102504035-102505002	H1-hESC	embryonic stem cell:	n/a	n/a
17	JUND	chr8:102503510-102505372	MCF-7	breast:	n/a	n/a
18	TAF1	chr8:102503770-102505122	H1-hESC	embryonic stem cell:	n/a	n/a
19	TEAD4	chr8:102504107-102505204	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr8:102503703-102506870	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP4	chr8:102504112-102504883	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF12	chr8:102504069-102505426	ECC-1	luminal epithelium:	n/a	n/a
23	HDAC2	chr8:102503502-102507679	MCF-7	breast:	n/a	chr8:102505260-102505274
24	MYC	chr8:102504382-102505090	MCF-7	breast:	n/a	n/a
25	MAX	chr8:102503816-102505124	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr8:102504129-102506801	HCT-116	colon:	n/a	n/a
27	GATA3	chr8:102503623-102507890	MCF-7	breast:	n/a	n/a
28	FOXA1	chr8:102504160-102505088	T-47D	breast:	n/a	n/a
29	TCF7L2	chr8:102504420-102506551	HCT-116	colon:	n/a	n/a
30	TCF12	chr8:102504092-102506600	ECC-1	luminal epithelium:	n/a	n/a
31	MYC	chr8:102504436-102504649	MCF-7	breast:	n/a	n/a
32	EGR1	chr8:102504162-102506494	HCT-116	colon:	n/a	chr8:102505683-102505696 chr8:102505682-102505697 chr8:102505715-102505725 chr8:102505684-102505694 chr8:102505683-102505696 chr8:102505684-102505695 chr8:102505684-102505693 chr8:102505682-102505696 chr8:102505535-102505550 chr8:102505683-102505693 chr8:102505683-102505696 chr8:102505684-102505694
33	NFIC	chr8:102504514-102505216	ECC-1	luminal epithelium:	n/a	n/a
34	FOXM1	chr8:102504505-102505313	ECC-1	luminal epithelium:	n/a	n/a
35	SP1	chr8:102504304-102505139	H1-hESC	embryonic stem cell:	n/a	chr8:102504600-102504621
36	TAF1	chr8:102503726-102506926	MCF-7	breast:	n/a	n/a
37	MAX	chr8:102504149-102504749	H1-hESC	embryonic stem cell:	n/a	n/a
38	PML	chr8:102503530-102507277	MCF-7	breast:	n/a	n/a
39	MAX	chr8:102503748-102505248	ECC-1	luminal epithelium:	n/a	n/a
40	ELF1	chr8:102503851-102507181	MCF-7	breast:	n/a	chr8:102506103-102506115
41	YY1	chr8:102504147-102505205	ECC-1	luminal epithelium:	n/a	n/a
42	HA-E2F1	chr8:102503856-102506832	MCF-7	breast:	n/a	chr8:102505795-102505805 chr8:102505964-102505976 chr8:102506157-102506166 chr8:102505033-102505043 chr8:102506159-102506171 chr8:102504601-102504610 chr8:102505821-102505830
43	POLR2A	chr8:102503712-102506756	H1-hESC	embryonic stem cell:	n/a	n/a
44	TBP	chr8:102503615-102506755	H1-hESC	embryonic stem cell:	n/a	n/a
45	SRF	chr8:102504141-102505232	ECC-1	luminal epithelium:	n/a	n/a
46	CEBPB	chr8:102503644-102505433	MCF-7	breast:	n/a	chr8:102504136-102504145 chr8:102504602-102504610 chr8:102504136-102504145 chr8:102504136-102504145 chr8:102504135-102504146 chr8:102504134-102504147
47	MAX	chr8:102503652-102507680	MCF-7	breast:	n/a	chr8:102506109-102506119 chr8:102507319-102507328
48	RAD21	chr8:102502828-102505295	MCF-7	breast:	n/a	n/a
49	NFIC	chr8:102504410-102505286	ECC-1	luminal epithelium:	n/a	n/a
50	TAF1	chr8:102504143-102505162	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:102504501-102504551	HEEpiC	esophagus:	n/a
2	chr8:102504501-102504551	A549	lung:	n/a
3	chr8:102504501-102504551	MCF10A-Er-Src	breast:	n/a
4	chr8:102504501-102504551	HUVEC	blood vessel:	n/a
5	chr8:102504501-102504551	HMEC	breast:	n/a
6	chr8:102504501-102504551	NT2-D1	testis:	n/a
7	chr8:102504501-102504551	PFSK-1	brain:	n/a
8	chr8:102504501-102504551	ovcar-3	ovarian:	n/a
9	chr8:102504501-102504551	SK-N-SH	brain:	n/a
10	chr8:102504501-102504551	GM19239	blood:	n/a
11	chr8:102504501-102504551	SAEC	small airway:	n/a
12	chr8:102504501-102504551	HCM	heart:	n/a
13	chr8:102504501-102504551	GM12878	blood:	n/a
14	chr8:102504501-102504551	SKMC	muscle:	n/a
15	chr8:102504501-102504551	HAEpiC	amniotic membrane:	n/a
16	chr8:102504501-102504551	ProgFib	skin:	n/a
17	chr8:102504501-102504551	GM06990	blood:	n/a
18	chr8:102504501-102504551	LNCaP	prostate:	n/a
19	chr8:102504501-102504551	AG09309	skin:	n/a
20	chr8:102504501-102504551	RPTEC	kidney:	n/a
21	chr8:102504501-102504551	Hela-S3	cervix:	n/a
22	chr8:102504501-102504551	AG09319	gingival:	n/a
23	chr8:102504501-102504551	HCF	heart:	n/a
24	chr8:102504501-102504551	HRPEpiC	eye:	n/a
25	chr8:102504501-102504551	SK-N-MC	brain:	n/a
26	chr8:102504501-102504551	IMR90	lung:	fetal
27	chr8:102504501-102504551	GM12891	blood:	n/a
28	chr8:102504501-102504551	HCT-116	colon:	n/a
29	chr8:102504501-102504551	AG04450	lung:	fetal
30	chr8:102504501-102504551	HRE	kidney:	n/a
31	chr8:102504501-102504551	T-47D	breast:	n/a
32	chr8:102504501-102504551	Jurkat	blood:	n/a
33	chr8:102504501-102504551	GM12892	blood:	n/a
34	chr8:102504501-102504551	HEK293	kidney:	embryo
35	chr8:102504501-102504551	Caco-2	colon:	n/a
36	chr8:102504501-102504551	NH-A	brain:	n/a
37	chr8:102504501-102504551	HL-60	blood:	n/a
38	chr8:102504501-102504551	NHBE	bronchial:	n/a
39	chr8:102504501-102504551	AG10803	skin:	n/a
40	chr8:102504501-102504551	CMK	blood:	n/a
41	chr8:102504501-102504551	HPAEpiC	pulmonary alveolar:	n/a
42	chr8:102504501-102504551	MCF-7	breast:	n/a
43	chr8:102504501-102504551	U87	brain:	n/a
44	chr8:102504501-102504551	HRCEpiC	kidney:	n/a
45	chr8:102504501-102504551	NB4	blood:	n/a
46	chr8:102504501-102504551	H1-hESC	embryonic stem cell:	embryo
47	chr8:102504501-102504551	BE2_C	brain:	n/a
48	chr8:102504501-102504551	BJ	skin:	n/a
49	chr8:102504501-102504551	AG04449	skin:	fetal
50	chr8:102504501-102504551	HNPCEpiC	eye:	n/a

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:102337542..102358418-chr8:102498403..102509669,87	MCF-7	breast:
2	chr8:102502419..102504596-chr8:103229752..103231759,2	MCF-7	breast:
3	chr8:102503375..102506182-chrX:131157229..131158900,2	MCF-7	breast:
4	chr8:102366174..102402527-chr8:102495873..102512355,186	MCF-7	breast:
5	chr8:102402569..102408629-chr8:102502856..102508138,9	MCF-7	breast:
6	chr8:102503148..102509288-chr8:102639386..102649682,19	MCF-7	breast:
7	chr8:102326841..102405579-chr8:102488885..102536287,493	MCF-7	breast:
8	chr20:34251761..34253653-chr8:102503473..102505454,2	MCF-7	breast:
9	chr14:77769535..77771801-chr8:102503565..102505939,2	MCF-7	breast:
10	chr8:101963437..101966002-chr8:102504063..102506210,2	MCF-7	breast:
11	chr8:82753265..82755662-chr8:102503401..102505345,2	MCF-7	breast:
12	chr8:101959027..101961096-chr8:102504043..102506197,2	MCF-7	breast:
13	chr8:102503544..102506939-chr8:103817000..103821587,6	MCF-7	breast:
14	chr8:102504268..102505953-chr9:132256478..132258911,2	MCF-7	breast:
15	chr8:99305569..99307437-chr8:102502783..102504954,2	MCF-7	breast:
16	chr8:102504533..102507820-chr9:114657351..114661372,3	MCF-7	breast:
17	chr8:101962743..101965419-chr8:102503766..102506202,3	MCF-7	breast:
18	chr3:49057353..49060318-chr8:102504216..102506462,2	MCF-7	breast:
19	chr6:30583199..30584838-chr8:102502363..102505193,2	MCF-7	breast:
20	chr17:58676308..58677992-chr8:102503375..102505065,2	MCF-7	breast:
21	chr8:102499850..102508532-chr8:102642696..102652505,26	MCF-7	breast:

No data

Variant related genes	Relation type
GRHL2	TF binding region
GRHL2	CpG island
ENSG00000271560	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000254063	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000244462	Chromatin interaction
ENSG00000048392	Chromatin interaction
ENSG00000104497	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000253669	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000009830	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000214078	Chromatin interaction
ENSG00000170836	Chromatin interaction
ENSG00000134602	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000104361	Chromatin interaction
ENSG00000228224	Chromatin interaction
ENSG00000148154	Chromatin interaction
ENSG00000083307	Chromatin interaction
ENSG00000204054	Chromatin interaction
ENSG00000253644	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2847730	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs475304	0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs509390	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[ASN][1000 genomes]
rs514588	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs515622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs523244	0.86[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs534285	1.00[JPT][hapmap]
rs537658	0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs541226	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs560043	1.00[JPT][hapmap]
rs561626	0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs568894	0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs589919	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs624013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs680890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs687909	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024652	chr8:101802121-102587124	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
2	nsv539699	chr8:101802121-102587124	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
3	nsv891229	chr8:102490380-102511670	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102497400-102506000	Weak transcription	Ovary	ovary
2	chr8:102501200-102507600	Active TSS	Placenta Amnion	Placenta Amnion
3	chr8:102503000-102504800	Bivalent/Poised TSS	Fetal Lung	lung
4	chr8:102503000-102506800	Active TSS	Esophagus	oesophagus
5	chr8:102503400-102507400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr8:102503400-102507600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr8:102503600-102504800	Bivalent Enhancer	Brain Hippocampus Middle	brain
8	chr8:102503600-102505000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr8:102503600-102505600	Bivalent/Poised TSS	Fetal Kidney	kidney
10	chr8:102503600-102507200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr8:102503600-102507200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:102503600-102507200	Bivalent Enhancer	Fetal Brain Male	brain
13	chr8:102503600-102507400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr8:102503600-102507600	Active TSS	Pancreas	Pancrea
15	chr8:102503800-102504600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr8:102503800-102504600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr8:102503800-102504600	Bivalent Enhancer	Brain Anterior Caudate	brain
18	chr8:102503800-102504600	Active TSS	Colonic Mucosa	Colon
19	chr8:102503800-102504600	Flanking Active TSS	HMEC	breast
20	chr8:102503800-102505200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
21	chr8:102503800-102505200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
22	chr8:102503800-102506000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr8:102503800-102506200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr8:102503800-102506400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:102503800-102506800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr8:102503800-102506800	Active TSS	Gastric	stomach
27	chr8:102503800-102507000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr8:102503800-102507000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr8:102503800-102507000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr8:102503800-102507200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr8:102503800-102507200	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr8:102503800-102507200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
33	chr8:102503800-102507400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr8:102503800-102507400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr8:102503800-102507600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr8:102504000-102504600	Bivalent Enhancer	Liver	Liver
37	chr8:102504000-102505000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
38	chr8:102504000-102505000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
39	chr8:102504000-102505200	Bivalent Enhancer	Fetal Heart	heart
40	chr8:102504000-102505400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
41	chr8:102504000-102505400	Bivalent/Poised TSS	Fetal Thymus	thymus
42	chr8:102504000-102506000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
43	chr8:102504000-102506000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
44	chr8:102504000-102506800	Bivalent/Poised TSS	Stomach Mucosa	stomach
45	chr8:102504000-102506800	Bivalent/Poised TSS	Thymus	Thymus
46	chr8:102504000-102507000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr8:102504000-102507800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr8:102504200-102504600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
49	chr8:102504200-102504600	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
50	chr8:102504200-102504600	Bivalent Enhancer	Right Ventricle	heart

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