Variant report

Variant	rs12492289
Chromosome Location	chr3:194958879-194958880
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194943164..194945109-chr3:194956482..194959428,2	K562	blood:
2	chr3:194942154..194945109-chr3:194956482..194959428,3	K562	blood:
3	chr3:194956917..194959266-chr3:194967812..194970352,2	K562	blood:
4	chr3:194956680..194958904-chr3:194960408..194963314,3	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:36)

rs_ID	r²[population]
rs10933702	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933703	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917438	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918143	0.86[AMR][1000 genomes]
rs11919965	0.85[EUR][1000 genomes]
rs11928199	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12485800	0.86[EUR][1000 genomes]
rs12486168	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486220	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486835	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488616	0.81[EUR][1000 genomes]
rs12491426	0.81[EUR][1000 genomes]
rs12491902	0.81[EUR][1000 genomes]
rs12492644	0.85[EUR][1000 genomes]
rs12493888	0.81[EUR][1000 genomes]
rs12495659	0.81[EUR][1000 genomes]
rs12496628	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497906	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12498063	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35899174	0.95[EUR][1000 genomes]
rs56835677	0.81[EUR][1000 genomes]
rs58113840	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59579668	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61022222	0.81[EUR][1000 genomes]
rs6437466	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66510151	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67388686	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67484513	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777904	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6785108	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790425	0.92[AMR][1000 genomes]
rs6804467	0.85[EUR][1000 genomes]
rs72499624	0.81[EUR][1000 genomes]
rs73069019	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7642127	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999331	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
17	nsv984539	chr3:194945800-194984579	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194940600-194959000	Weak transcription	Right Ventricle	heart
2	chr3:194944600-194959000	Weak transcription	Ovary	ovary
3	chr3:194945200-194959200	Weak transcription	NHLF	lung
4	chr3:194945400-194959200	Weak transcription	Osteobl	bone
5	chr3:194945400-194971600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:194945600-194959000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:194946000-194959000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:194946000-194971400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:194947000-194959000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:194947600-194962200	Weak transcription	Hela-S3	cervix
11	chr3:194947800-194959000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:194947800-194959400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:194947800-194961200	Weak transcription	Gastric	stomach
14	chr3:194948000-194959000	Weak transcription	Lung	lung
15	chr3:194948200-194959000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:194948200-194959200	Weak transcription	HUVEC	blood vessel
17	chr3:194948400-194959400	Weak transcription	Fetal Brain Female	brain
18	chr3:194949000-194959000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:194955000-194973200	Weak transcription	NH-A	brain
20	chr3:194955400-194959200	Weak transcription	Fetal Lung	lung
21	chr3:194956400-194959000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:194956400-194966800	Weak transcription	HSMM	muscle
23	chr3:194956600-194972800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:194957000-194959200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
25	chr3:194957000-194959600	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr3:194957200-194971800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:194957200-194972800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:194957400-194959000	Weak transcription	NHDF-Ad	bronchial
29	chr3:194957400-194979800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:194957600-194975400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:194958000-194959000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:194958000-194959000	Weak transcription	Right Atrium	heart
33	chr3:194958000-194959400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:194958000-194960800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:194958000-194966600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:194958200-194959000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:194958200-194959000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:194958200-194959000	Weak transcription	Primary T cells from cord blood	blood
39	chr3:194958200-194959000	Weak transcription	Spleen	Spleen
40	chr3:194958200-194959200	Weak transcription	Adipose Nuclei	Adipose
41	chr3:194958200-194964000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:194958200-194964600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:194958200-194966200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:194958200-194966200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:194958200-194966400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:194958200-194967000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:194958200-194967000	Weak transcription	Dnd41	blood
48	chr3:194958200-194967600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:194958400-194959000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:194958400-194959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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