Variant report

Variant	rs3767025
Chromosome Location	chr1:78428851-78428852
allele	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	POLR2A	chr1:78428731-78428942	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:78423763-78431474	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78428375..78429154-chr1:78579795..78580540,2	MCF-7	breast:
2	chr1:78428722..78431621-chr1:78443319..78444830,2	MCF-7	breast:
3	chr1:78427480..78429581-chr1:78433506..78436047,2	MCF-7	breast:

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000162613	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1039863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10735751	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10873961	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10873962	0.81[ASN][1000 genomes]
rs10873963	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.81[ASN][1000 genomes]
rs11162401	1.00[ASN][1000 genomes]
rs1166696	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1166699	0.93[ASN][1000 genomes]
rs1166700	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11805942	1.00[ASN][1000 genomes]
rs11806130	0.98[ASN][1000 genomes]
rs11811805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1510244	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17101101	1.00[ASN][1000 genomes]
rs1749911	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1749913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1780044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1780045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1780047	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1780048	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1780052	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296454	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3736909	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3767024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3790586	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4083559	0.90[ASN][1000 genomes]
rs4107671	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4483454	0.93[ASN][1000 genomes]
rs4543852	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4631748	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs4949823	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6424648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6424653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6604878	0.86[CHB][hapmap]
rs6675105	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6680447	0.86[ASN][1000 genomes]
rs6699513	0.81[ASN][1000 genomes]
rs6702465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72685363	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72685364	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72685368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7520255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7523874	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7524504	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7547599	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9661687	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9662129	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9729146	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78405800-78432200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:78405800-78442200	Strong transcription	Fetal Thymus	thymus
3	chr1:78406000-78436200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:78406600-78436200	Strong transcription	Liver	Liver
5	chr1:78406600-78440600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:78406800-78436400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:78407000-78434400	Strong transcription	Dnd41	blood
8	chr1:78407000-78437200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:78407400-78432800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:78407400-78436600	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr1:78407400-78437600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:78407400-78437800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr1:78407600-78435400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:78407600-78435600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:78407600-78437200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:78407800-78435400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:78407800-78436800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr1:78407800-78437200	Strong transcription	Placenta	Placenta
19	chr1:78408000-78437600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:78408200-78434200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:78408400-78436400	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:78408400-78439600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:78408600-78437000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:78409600-78432000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:78409600-78432200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:78409600-78437200	Strong transcription	Hela-S3	cervix
27	chr1:78410000-78433800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:78411800-78438200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:78412400-78434800	Strong transcription	Fetal Lung	lung
30	chr1:78412800-78434800	Strong transcription	Fetal Brain Female	brain
31	chr1:78413000-78432600	Strong transcription	Primary T cells from cord blood	blood
32	chr1:78415000-78434200	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:78415000-78435800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:78415000-78437200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:78415200-78430600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr1:78415600-78434800	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr1:78415800-78432400	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:78415800-78434800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:78415800-78435200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:78415800-78436400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:78415800-78436800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:78415800-78437600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:78415800-78440200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:78416000-78432400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:78416400-78437400	Strong transcription	K562	blood
46	chr1:78416400-78438200	Strong transcription	HMEC	breast
47	chr1:78416600-78430600	Strong transcription	NHLF	lung
48	chr1:78416600-78434800	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:78416600-78435400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:78416800-78432200	Strong transcription	Thymus	Thymus

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