Variant report

Variant	rs13091531
Chromosome Location	chr3:156894096-156894097
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:156892463-156894182	Hela-S3	cervix:	n/a	n/a
2	ZNF263	chr3:156893685-156894420	HEK293-T-REx	kidney:	n/a	chr3:156894063-156894084
3	MXI1	chr3:156891834-156895033	IMR90	lung:	n/a	n/a
4	TCF7L2	chr3:156892159-156894170	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:156891606-156894394	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr3:156891994-156894121	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr3:156891521-156894953	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:156891771-156894178	K562	blood:	n/a	n/a
9	POLR2A	chr3:156891710-156894209	GM12878	blood:	n/a	n/a
10	PML	chr3:156891946-156894196	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:156891642-156894205	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr3:156891716-156894206	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:156891715-156894302	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:156891784-156894152	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:156891903-156894217	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:156893850-156894205	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:156893951-156894246	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr3:156891855-156894379	IMR90	lung:	n/a	n/a
19	POLR2A	chr3:156891848-156894273	SK-N-SH	brain:	n/a	n/a
20	HCFC1	chr3:156891636-156894761	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr3:156893992-156894190	K562	blood:	n/a	n/a
22	POLR2A	chr3:156891574-156894151	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:156891947-156894233	GM18505	blood:	n/a	n/a
24	POLR2A	chr3:156891827-156894156	K562	blood:	n/a	n/a
25	POLR2A	chr3:156894086-156894180	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156891687..156894320-chr3:157219306..157221888,3	MCF-7	breast:
2	chr3:156347077..156349787-chr3:156893431..156895606,2	K562	blood:
3	chr3:156877577..156878787-chr3:156892042..156894243,14	HCT-116	colon:
4	chr3:156271607..156273392-chr3:156891262..156894145,2	K562	blood:
5	chr3:156533499..156536526-chr3:156891417..156894235,3	MCF-7	breast:
6	chr19:22668311..22668965-chr3:156893491..156894131,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP146	TF binding region
ENSG00000114850	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000197415	Chromatin interaction
ENSG00000240875	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10440022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs11917697	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12634613	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12696046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13064954	1.00[CEU][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13072252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13072425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs13076599	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13078493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13084377	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13090731	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13093524	0.90[AMR][1000 genomes]
rs13316165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13319063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13319093	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13321401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs13324111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13325320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13326278	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13326287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16827382	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs28447380	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28513929	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28671546	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34154019	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34300533	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34508886	0.93[AMR][1000 genomes]
rs35196422	0.86[EUR][1000 genomes]
rs35295311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35988323	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3749215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66686295	0.89[EUR][1000 genomes]
rs6764639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71310497	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71310500	0.93[AMR][1000 genomes]
rs71310501	0.93[AMR][1000 genomes]
rs7613866	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9814142	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814609	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817490	1.00[CEU][hapmap]
rs9817693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9821290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs9827476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9829650	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9830661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856475	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9856588	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9863805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9868982	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9870220	0.85[JPT][hapmap]

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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv520331	chr3:156858300-156915650	Flanking Active TSS Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 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	chr3:156891800-156894200	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:156891800-156894200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:156891800-156894400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:156891800-156894400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:156891800-156894400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:156891800-156894400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:156892000-156894200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:156892000-156894200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:156892000-156894400	Active TSS	Brain Germinal Matrix	brain
10	chr3:156892000-156894400	Active TSS	Right Ventricle	heart
11	chr3:156892200-156894200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr3:156892200-156894200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:156892200-156894200	Active TSS	Fetal Stomach	stomach
14	chr3:156892200-156894400	Active TSS	Stomach Mucosa	stomach
15	chr3:156892400-156894200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:156892400-156894200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:156892400-156894200	Active TSS	NHDF-Ad	bronchial
18	chr3:156892400-156894200	Active TSS	NHLF	lung
19	chr3:156892400-156894400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:156892400-156894600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:156892400-156895000	Active TSS	GM12878-XiMat	blood
22	chr3:156892600-156894200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:156892600-156894200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:156892600-156894200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:156893000-156894400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:156893200-156894200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr3:156893200-156894400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr3:156893200-156894400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:156893400-156894200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr3:156893400-156894200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr3:156893400-156894400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:156893400-156894600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:156893600-156894200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:156893600-156894200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:156893600-156894200	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr3:156893600-156894200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr3:156893600-156894400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:156893600-156894400	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr3:156893600-156894400	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr3:156893600-156894600	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr3:156893600-156894600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:156893600-156894600	Flanking Active TSS	HUVEC	blood vessel
43	chr3:156893800-156894200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:156893800-156894200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:156893800-156894200	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr3:156893800-156894200	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr3:156893800-156894200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr3:156893800-156894200	Enhancers	Gastric	stomach
49	chr3:156893800-156894200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr3:156893800-156894200	Flanking Active TSS	HSMMtube	muscle

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