Variant report

Variant	rs28464438
Chromosome Location	chr5:176939051-176939052
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	chr5:176938613-176939336	K562	blood:	n/a	n/a
2	POLR2A	chr5:176934713-176942234	K562	blood:	n/a	n/a
3	POLR2A	chr5:176938829-176939123	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
DOK3	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs28366804	1.00[YRI][hapmap]
rs28379386	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28392715	1.00[AMR][1000 genomes]
rs28396982	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[LWK][hapmap];1.00[YRI][hapmap];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]
rs28688891	1.00[AFR][1000 genomes];1.00[AMR][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[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv883166	chr5:176817636-176940384	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	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
10	nsv883174	chr5:176842474-176940384	Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Weak transcription 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	100 gene(s)	inside rSNPs	diseases
11	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
12	nsv1026103	chr5:176851182-176942552	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	nsv1018088	chr5:176861503-176942552	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription 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	80 gene(s)	inside rSNPs	diseases
14	nsv1028123	chr5:176861503-176949149	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
15	nsv537965	chr5:176861503-176949149	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	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
17	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
18	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
19	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:176925600-176942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:176927000-176942000	Weak transcription	Fetal Kidney	kidney
3	chr5:176928400-176941000	Weak transcription	Fetal Brain Male	brain
4	chr5:176928600-176939600	Weak transcription	NHDF-Ad	bronchial
5	chr5:176930600-176942400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:176934000-176942600	Strong transcription	Fetal Intestine Small	intestine
7	chr5:176934200-176941800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:176934400-176941000	Strong transcription	Brain Germinal Matrix	brain
9	chr5:176934600-176941600	Strong transcription	Fetal Stomach	stomach
10	chr5:176934800-176941800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:176935000-176942000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:176935200-176942400	Strong transcription	Fetal Brain Female	brain
13	chr5:176935200-176942600	Strong transcription	NHLF	lung
14	chr5:176935400-176942000	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:176936200-176942800	Weak transcription	Stomach Mucosa	stomach
16	chr5:176936400-176942400	Weak transcription	Fetal Heart	heart
17	chr5:176936800-176942600	Strong transcription	NHEK	skin
18	chr5:176936800-176942800	Weak transcription	Right Atrium	heart
19	chr5:176937000-176941800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:176937000-176942000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:176937000-176942400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:176937000-176942800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:176937200-176941200	Strong transcription	Dnd41	blood
24	chr5:176937200-176942400	Strong transcription	Aorta	Aorta
25	chr5:176937400-176940800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:176937400-176941000	Strong transcription	Psoas Muscle	Psoas
27	chr5:176937400-176941200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:176937400-176941400	Strong transcription	Gastric	stomach
29	chr5:176937400-176941600	Strong transcription	Lung	lung
30	chr5:176937400-176941600	Strong transcription	Right Ventricle	heart
31	chr5:176937400-176942000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:176937400-176942200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:176937400-176942200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:176937400-176942400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:176937400-176942400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:176937400-176942400	Strong transcription	Esophagus	oesophagus
37	chr5:176937400-176942400	Strong transcription	Thymus	Thymus
38	chr5:176937400-176942400	Strong transcription	Osteobl	bone
39	chr5:176937400-176942600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:176937400-176942600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:176937400-176942600	Strong transcription	Brain Hippocampus Middle	brain
42	chr5:176937400-176942600	Strong transcription	A549	lung
43	chr5:176937400-176942800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:176937400-176943200	Genic enhancers	Spleen	Spleen
45	chr5:176937600-176939600	Strong transcription	Liver	Liver
46	chr5:176937600-176940200	Strong transcription	HMEC	breast
47	chr5:176937600-176941400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr5:176937600-176941400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr5:176937600-176941400	Strong transcription	Brain Angular Gyrus	brain
50	chr5:176937600-176941600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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