Variant report

Variant	rs28688891
Chromosome Location	chr5:176950879-176950880
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	chr5:176950508-176951908	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr5:176950646-176951360	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:176950724-176951836	K562	blood:	n/a	n/a
4	POLR2A	chr5:176950649-176951144	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr5:176950753-176951124	K562	blood:	n/a	n/a
6	POLR2A	chr5:176950873-176951058	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr5:176950676-176951182	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr5:176950684-176950919	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:176950866-176951086	K562	blood:	n/a	n/a
10	POLR2A	chr5:176950300-176953321	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:176943048..176946305-chr5:176949965..176953644,6	MCF-7	breast:

Variant related genes	Relation type
FAM193B	TF binding region
ENSG00000183258	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs28379386	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28392715	1.00[AMR][1000 genomes]
rs28396982	1.00[AMR][1000 genomes]
rs28464438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28483466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28491669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28494836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28565502	0.84[AFR][1000 genomes]
rs28587302	1.00[AMR][1000 genomes]
rs28613023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28615269	1.00[AMR][1000 genomes]
rs28630512	0.94[AFR][1000 genomes]
rs28723606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs337387	1.00[AMR][1000 genomes]
rs337399	1.00[AMR][1000 genomes]
rs388783	1.00[AMR][1000 genomes]
rs4976650	1.00[AMR][1000 genomes]
rs5013573	1.00[AMR][1000 genomes]
rs58021881	1.00[AMR][1000 genomes]
rs6600953	1.00[AMR][1000 genomes]
rs7444245	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv883160	chr5:176740996-176952919	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
4	nsv883161	chr5:176754722-176958397	Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv1020334	chr5:176779108-176954933	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
6	nsv883164	chr5:176780545-177003616	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
7	esv1816147	chr5:176787037-176966509	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv883170	chr5:176824137-176952919	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
9	nsv883175	chr5:176842474-176952919	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
10	nsv883177	chr5:176868358-177003616	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
11	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer 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	78 gene(s)	inside rSNPs	diseases
12	nsv984570	chr5:176923414-176956300	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv5147	chr5:176938196-176983018	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 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	chr5:176944800-176951400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:176944800-176951600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:176944800-176952000	Weak transcription	Psoas Muscle	Psoas
4	chr5:176944800-176953000	Weak transcription	Fetal Brain Male	brain
5	chr5:176944800-176955000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:176944800-176963400	Weak transcription	Right Atrium	heart
7	chr5:176944800-176972800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:176946000-176966200	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:176946000-176968000	Strong transcription	Fetal Thymus	thymus
10	chr5:176946000-176970000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:176946200-176966200	Strong transcription	Fetal Brain Female	brain
12	chr5:176946200-176966200	Strong transcription	Fetal Intestine Small	intestine
13	chr5:176946200-176966800	Strong transcription	Fetal Stomach	stomach
14	chr5:176946200-176968000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:176946200-176969800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:176946200-176970200	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr5:176946200-176971000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr5:176946400-176957200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:176946400-176957800	Weak transcription	Fetal Heart	heart
20	chr5:176946400-176960200	Strong transcription	Aorta	Aorta
21	chr5:176946400-176961200	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr5:176946400-176964000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr5:176946400-176964200	Strong transcription	A549	lung
24	chr5:176946400-176965000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:176946400-176966200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr5:176946400-176966800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:176946400-176966800	Strong transcription	Fetal Lung	lung
28	chr5:176946400-176969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:176946400-176970000	Strong transcription	Thymus	Thymus
30	chr5:176946600-176951600	Strong transcription	Stomach Smooth Muscle	stomach
31	chr5:176946600-176956400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr5:176946600-176956600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:176946600-176960800	Strong transcription	Liver	Liver
34	chr5:176946600-176961800	Strong transcription	Colon Smooth Muscle	Colon
35	chr5:176946600-176962400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:176946600-176963000	Strong transcription	Colonic Mucosa	Colon
37	chr5:176946600-176963800	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:176946600-176963800	Strong transcription	Osteobl	bone
39	chr5:176946600-176965200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:176946600-176966400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:176946600-176966600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr5:176946600-176966800	Strong transcription	Fetal Intestine Large	intestine
43	chr5:176946600-176969800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:176946800-176957200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:176946800-176963400	Strong transcription	Placenta	Placenta
46	chr5:176946800-176963600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:176946800-176963800	Strong transcription	NHLF	lung
48	chr5:176946800-176967600	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr5:176946800-176977200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:176947000-176966200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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