Variant report

Variant	rs57287670
Chromosome Location	chr3:194930511-194930512
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	TCF12	chr3:194930437-194931947	SK-N-SH	brain:	n/a	chr3:194931446-194931453 chr3:194931206-194931213
2	CTCF	chr3:194930440-194930590	HCPEpiC	choroid plexus:	n/a	n/a
3	NFIC	chr3:194930487-194931928	SK-N-SH	brain:	n/a	chr3:194931220-194931236 chr3:194931219-194931236
4	EP300	chr3:194930487-194931782	SK-N-SH	brain:	n/a	n/a
5	EP300	chr3:194930501-194930946	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
XXYLT1	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs58699597	1.00[AFR][1000 genomes]
rs59208268	0.95[AFR][1000 genomes]
rs61022222	0.91[AFR][1000 genomes]
rs73063169	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
12	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
13	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
14	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
20	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194917600-194930600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:194918800-194945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:194919400-194945200	Weak transcription	Thymus	Thymus
4	chr3:194920000-194930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:194921000-194941600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:194924600-194930800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:194924600-194931800	Enhancers	Placenta	Placenta
8	chr3:194925600-194931000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:194925800-194930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:194926000-194930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:194926200-194930600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:194926200-194930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:194926400-194930600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:194926400-194930600	Weak transcription	Fetal Kidney	kidney
15	chr3:194926400-194930800	Weak transcription	Stomach Mucosa	stomach
16	chr3:194926400-194930800	Weak transcription	NHEK	skin
17	chr3:194926400-194931400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:194926400-194942600	Weak transcription	Small Intestine	intestine
19	chr3:194926400-194947600	Weak transcription	Gastric	stomach
20	chr3:194926600-194930600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:194926600-194930600	Weak transcription	Fetal Brain Female	brain
22	chr3:194926600-194933400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:194926600-194942800	Weak transcription	Hela-S3	cervix
24	chr3:194927600-194931800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:194927800-194931800	Enhancers	Fetal Thymus	thymus
26	chr3:194928200-194931200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:194928400-194930600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:194928400-194930800	Enhancers	NH-A	brain
29	chr3:194928400-194931000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:194928400-194931200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:194928400-194931800	Enhancers	Left Ventricle	heart
32	chr3:194928400-194932000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr3:194928400-194932000	Enhancers	Brain Germinal Matrix	brain
34	chr3:194928400-194932600	Enhancers	Ovary	ovary
35	chr3:194928400-194932600	Enhancers	NHLF	lung
36	chr3:194928600-194930600	Enhancers	HepG2	liver
37	chr3:194928600-194930800	Enhancers	Fetal Lung	lung
38	chr3:194928600-194931200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:194928600-194931200	Enhancers	Spleen	Spleen
40	chr3:194928600-194931800	Enhancers	Right Ventricle	heart
41	chr3:194928600-194932200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:194928600-194932400	Enhancers	Fetal Heart	heart
43	chr3:194928600-194932600	Enhancers	Fetal Stomach	stomach
44	chr3:194928600-194933600	Enhancers	Lung	lung
45	chr3:194928800-194931200	Flanking Active TSS	NHDF-Ad	bronchial
46	chr3:194928800-194931600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:194928800-194931800	Enhancers	Brain Hippocampus Middle	brain
48	chr3:194929000-194930800	Enhancers	Colonic Mucosa	Colon
49	chr3:194929000-194931200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr3:194929000-194931200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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