Variant report

Variant	rs13228828
Chromosome Location	chr7:5473107-5473108
allele	C/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	chr7:5473104-5473148	MCF-7	breast:	n/a	n/a
2	POLR2A	chr7:5472883-5473334	HepG2	liver:	n/a	n/a
3	CBX3	chr7:5472814-5473217	K562	blood:	n/a	n/a
4	CBX3	chr7:5472726-5473160	K562	blood:	n/a	n/a
5	POLR2A	chr7:5472876-5473243	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:5462669-5473356	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:5472592-5473334	HepG2	liver:	n/a	n/a
8	POLR2A	chr7:5472827-5473398	HL-60	blood:	n/a	n/a
9	POLR2A	chr7:5472909-5473294	K562	blood:	n/a	n/a
10	POLR2A	chr7:5472826-5473220	HepG2	liver:	n/a	n/a
11	RCOR1	chr7:5473035-5473107	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:5472753-5473182	HepG2	liver:	n/a	n/a
13	HEY1	chr7:5473047-5473331	HepG2	liver:	n/a	n/a
14	KAP1	chr7:5472671-5473294	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5471770..5473767-chr7:5475636..5477605,3	K562	blood:
2	chr7:5472806..5475525-chr7:5495796..5497629,2	K562	blood:

Variant related genes	Relation type
ENSG00000234432	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10252993	1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10281062	1.00[JPT][hapmap]
rs13229269	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13232196	0.82[AMR][1000 genomes]
rs13242211	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28498371	0.96[ASN][1000 genomes]
rs28510321	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4720628	0.92[AFR][1000 genomes]
rs4720629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4724676	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56809987	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59290379	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6651075	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6651076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
5	nsv887396	chr7:5305297-5475409	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
7	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
8	nsv533965	chr7:5370746-5548397	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
9	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv887401	chr7:5393243-5539958	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
11	nsv887402	chr7:5394951-5494677	Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
13	nsv887405	chr7:5409059-5552436	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
14	nsv887406	chr7:5414602-5552436	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
15	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
16	nsv887407	chr7:5432672-5605130	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	302 gene(s)	inside rSNPs	diseases
17	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
18	nsv508443	chr7:5447283-5501122	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
19	nsv526194	chr7:5452756-5592436	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	278 gene(s)	inside rSNPs	diseases
20	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
21	nsv984498	chr7:5469767-5506036	Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5469400-5474400	Weak transcription	Aorta	Aorta
2	chr7:5469800-5475600	Weak transcription	Fetal Kidney	kidney
3	chr7:5470000-5481400	Weak transcription	HSMMtube	muscle
4	chr7:5470200-5481000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:5470200-5491800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr7:5470400-5475000	Weak transcription	NH-A	brain
7	chr7:5470400-5477000	Weak transcription	Brain Angular Gyrus	brain
8	chr7:5470400-5477000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:5470400-5477800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr7:5470400-5480800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:5470400-5481200	Weak transcription	Colonic Mucosa	Colon
12	chr7:5470400-5497600	Weak transcription	Right Atrium	heart
13	chr7:5470600-5479800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:5470600-5488000	Weak transcription	Colon Smooth Muscle	Colon
15	chr7:5471000-5476200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr7:5471000-5477400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr7:5471400-5473200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:5471400-5473800	Strong transcription	Fetal Intestine Large	intestine
19	chr7:5471600-5473200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr7:5471600-5487400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:5472200-5473400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:5472200-5479000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr7:5472400-5473200	Strong transcription	Esophagus	oesophagus
24	chr7:5472400-5473400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:5472400-5473400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
26	chr7:5472400-5473400	Strong transcription	Brain Hippocampus Middle	brain
27	chr7:5472600-5473200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:5472600-5473200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr7:5472600-5473200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:5472600-5473200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:5472600-5473200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr7:5472600-5473200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
33	chr7:5472600-5473200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr7:5472600-5473200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr7:5472600-5473200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:5472600-5473200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr7:5472600-5473200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:5472600-5473200	Strong transcription	Brain Germinal Matrix	brain
39	chr7:5472600-5473200	Strong transcription	Brain Substantia Nigra	brain
40	chr7:5472600-5473200	ZNF genes & repeats	Stomach Mucosa	stomach
41	chr7:5472600-5473200	ZNF genes & repeats	Hela-S3	cervix
42	chr7:5472600-5473200	ZNF genes & repeats	HMEC	breast
43	chr7:5472600-5473200	ZNF genes & repeats	NHEK	skin
44	chr7:5472600-5473200	Strong transcription	Osteobl	bone
45	chr7:5472600-5473400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:5472600-5473400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr7:5472600-5473400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
48	chr7:5472600-5473400	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr7:5472600-5473400	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr7:5472600-5473400	ZNF genes & repeats	Placenta	Placenta

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