Variant report

Variant	rs6541387
Chromosome Location	chr1:94148032-94148033
allele	A/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	POLR2A	chr1:94147920-94148175	Hela-S3	cervix:	n/a	n/a
2	STAT3	chr1:94147496-94148107	MCF10A-Er-Src	breast:	n/a	n/a
3	SMC3	chr1:94144843-94148119	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:94145532-94148138	HUVEC	blood vessel:	n/a	n/a
5	STAT3	chr1:94147884-94148106	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr1:94147986-94148286	K562	blood:	n/a	chr1:94148158-94148169
7	STAT3	chr1:94148032-94148111	MCF10A-Er-Src	breast:	n/a	n/a
8	CTCF	chr1:94146996-94148138	A549	lung:	n/a	chr1:94147374-94147387 chr1:94147374-94147387 chr1:94147846-94147854
9	RAD21	chr1:94145132-94148255	SK-N-SH	brain:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
10	MAZ	chr1:94145632-94148061	IMR90	lung:	n/a	n/a
11	CEBPB	chr1:94148016-94148308	IMR90	lung:	n/a	chr1:94148158-94148169

No.	Distal block	Cell Line	Cell type
1	chr1:94146501..94148043-chr1:94311466..94313377,2	MCF-7	breast:
2	chr1:93913059..93915471-chr1:94146480..94149352,2	MCF-7	breast:
3	chr1:94145898..94148493-chr1:94311257..94313086,3	MCF-7	breast:
4	chr1:94147624..94149289-chr1:94160364..94162854,2	MCF-7	breast:

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

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1011903	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164962	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11164963	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12057736	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12079723	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084853	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12092517	0.87[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12568405	1.00[JPT][hapmap]
rs1292929	0.91[ASN][1000 genomes]
rs1567791	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1772781	1.00[JPT][hapmap]
rs236266	1.00[JPT][hapmap]
rs236284	0.89[CEU][hapmap];0.86[ASN][1000 genomes]
rs236285	0.86[ASN][1000 genomes]
rs236287	0.89[CEU][hapmap];0.86[ASN][1000 genomes]
rs236288	0.91[ASN][1000 genomes]
rs236291	0.91[ASN][1000 genomes]
rs236292	0.88[ASN][1000 genomes]
rs236295	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236296	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs236301	0.91[ASN][1000 genomes]
rs236308	0.90[JPT][hapmap]
rs236312	1.00[JPT][hapmap]
rs236313	1.00[JPT][hapmap]
rs236343	0.89[JPT][hapmap]
rs3767979	0.89[JPT][hapmap]
rs3767991	1.00[JPT][hapmap]
rs399649	1.00[JPT][hapmap]
rs423493	1.00[JPT][hapmap]
rs61781002	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541386	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6541389	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657709	0.88[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6660740	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6701871	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6702036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6704479	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7513130	0.88[CEU][hapmap]
rs7519952	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798213	1.00[JPT][hapmap]
rs955470	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9659100	0.83[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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