Variant report

Variant	rs12493888
Chromosome Location	chr3:194927489-194927490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194924474..194927698-chr3:194929012..194931458,3	K562	blood:
2	chr3:194924290..194926220-chr3:194926449..194928088,2	K562	blood:
3	chr3:194926181..194927698-chr3:194929464..194931088,2	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11918143	0.95[EUR][1000 genomes]
rs11919965	0.84[EUR][1000 genomes]
rs11928199	0.95[EUR][1000 genomes]
rs12485800	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12486636	0.95[EUR][1000 genomes]
rs12488616	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12491426	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12491902	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12492289	0.81[EUR][1000 genomes]
rs12492644	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12494306	0.80[AMR][1000 genomes]
rs12495659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496459	0.93[AMR][1000 genomes]
rs12496628	0.85[EUR][1000 genomes]
rs12497444	0.95[EUR][1000 genomes]
rs12497906	0.95[EUR][1000 genomes]
rs35899174	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3796161	0.81[ASN][1000 genomes]
rs56281422	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56835677	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58113840	1.00[EUR][1000 genomes]
rs60677730	0.95[EUR][1000 genomes]
rs61022222	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66510151	1.00[EUR][1000 genomes]
rs67413252	0.90[EUR][1000 genomes]
rs67484513	1.00[EUR][1000 genomes]
rs6777904	1.00[EUR][1000 genomes]
rs6785108	0.85[EUR][1000 genomes]
rs6790425	0.95[EUR][1000 genomes]
rs6804467	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72499624	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72499625	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7642127	0.85[EUR][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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194916600-194929000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:194917200-194927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:194917600-194929400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:194917600-194930600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:194917800-194930400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:194918800-194945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:194919400-194945200	Weak transcription	Thymus	Thymus
8	chr3:194920000-194927800	Weak transcription	Pancreas	Pancrea
9	chr3:194920000-194930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:194921000-194941600	Weak transcription	Primary T cells from cord blood	blood
11	chr3:194924600-194930200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:194924600-194930800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:194924600-194931800	Enhancers	Placenta	Placenta
14	chr3:194925400-194927800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:194925400-194929000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:194925400-194929000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:194925600-194927600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:194925600-194928000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:194925600-194928600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:194925600-194928600	Weak transcription	Right Ventricle	heart
21	chr3:194925600-194929000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:194925600-194929000	Weak transcription	Right Atrium	heart
23	chr3:194925600-194931000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:194925800-194928800	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:194925800-194928800	Enhancers	NHDF-Ad	bronchial
26	chr3:194925800-194929800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:194925800-194930000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:194925800-194930400	Weak transcription	Brain Angular Gyrus	brain
29	chr3:194925800-194930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:194926000-194928400	Weak transcription	Brain Germinal Matrix	brain
31	chr3:194926000-194928400	Weak transcription	HSMM	muscle
32	chr3:194926000-194929800	Weak transcription	Liver	Liver
33	chr3:194926000-194930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr3:194926200-194928600	Weak transcription	Fetal Heart	heart
35	chr3:194926200-194928600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:194926200-194928800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:194926200-194929000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:194926200-194929000	Weak transcription	Colonic Mucosa	Colon
39	chr3:194926200-194929800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:194926200-194930600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:194926200-194930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:194926400-194927600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:194926400-194927600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:194926400-194927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:194926400-194927600	Weak transcription	Fetal Stomach	stomach
46	chr3:194926400-194927800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:194926400-194927800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:194926400-194927800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:194926400-194927800	Weak transcription	Adipose Nuclei	Adipose
50	chr3:194926400-194927800	Weak transcription	Fetal Thymus	thymus

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