Variant report

Variant	rs57293752
Chromosome Location	chr5:98112959-98112960
allele	A/G
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	chr5:98112853-98113685	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RGMB	TF binding region
RGMB-AS1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11954623	1.00[AMR][1000 genomes]
rs11957518	1.00[AMR][1000 genomes]
rs1508794	1.00[AMR][1000 genomes]
rs1508795	1.00[AMR][1000 genomes]
rs17166354	1.00[AMR][1000 genomes]
rs17166367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17166368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2035229	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2036691	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3952932	1.00[AMR][1000 genomes]
rs55660533	1.00[AMR][1000 genomes]
rs58710516	1.00[AMR][1000 genomes]
rs6890688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6895731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73151405	1.00[AMR][1000 genomes]
rs73151407	1.00[AMR][1000 genomes]
rs73151426	1.00[AMR][1000 genomes]
rs73151428	1.00[AMR][1000 genomes]
rs73151441	1.00[AMR][1000 genomes]
rs73151444	1.00[AMR][1000 genomes]
rs73151454	1.00[AMR][1000 genomes]
rs73151459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73151463	1.00[AMR][1000 genomes]
rs73151464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73151473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73153510	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7707936	1.00[AMR][1000 genomes]
rs906681	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers 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	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:98108800-98113000	Active TSS	NH-A	brain
3	chr5:98108800-98113000	Active TSS	NHEK	skin
4	chr5:98108800-98113800	Active TSS	Stomach Smooth Muscle	stomach
5	chr5:98109200-98113200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr5:98109400-98113400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:98109400-98113800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:98109600-98119200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:98109800-98114600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
10	chr5:98110200-98125200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
11	chr5:98110400-98113400	Transcr. at gene 5' and 3'	Osteobl	bone
12	chr5:98110400-98119200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:98110600-98113600	Active TSS	Fetal Intestine Small	intestine
14	chr5:98110600-98115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:98110800-98113400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:98110800-98113400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr5:98110800-98115200	Weak transcription	Lung	lung
18	chr5:98110800-98118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:98110800-98123200	Weak transcription	Aorta	Aorta
20	chr5:98111000-98115200	Weak transcription	Esophagus	oesophagus
21	chr5:98111000-98116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:98111000-98118600	Weak transcription	Gastric	stomach
23	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:98111200-98113400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:98111600-98113000	Active TSS	Duodenum Mucosa	Duodenum
27	chr5:98111600-98113200	Active TSS	HSMMtube	muscle
28	chr5:98111600-98116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
30	chr5:98111800-98113000	Active TSS	Fetal Intestine Large	intestine
31	chr5:98111800-98113200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr5:98111800-98113200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr5:98111800-98114000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr5:98111800-98114600	Weak transcription	Stomach Mucosa	stomach
35	chr5:98111800-98115200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr5:98111800-98116200	Weak transcription	Fetal Kidney	kidney
37	chr5:98111800-98119000	Weak transcription	Spleen	Spleen
38	chr5:98111800-98120200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr5:98112000-98113400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr5:98112000-98113400	Enhancers	Pancreas	Pancrea
41	chr5:98112000-98113600	Active TSS	GM12878-XiMat	blood
42	chr5:98112000-98114600	Weak transcription	Liver	Liver
43	chr5:98112000-98115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:98112000-98115400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr5:98112000-98115400	Weak transcription	Brain Substantia Nigra	brain
46	chr5:98112000-98116200	Weak transcription	A549	lung
47	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:98112200-98113400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:98112200-98114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:98112200-98114600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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