Variant report

Variant	rs2292138
Chromosome Location	chr12:123339712-123339713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123329734..123338030-chr12:123339120..123345153,11	MCF-7	breast:
2	chr12:55571372..55571892-chr12:123339417..123339937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10744422	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744434	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773627	0.87[EUR][1000 genomes]
rs10773657	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10847826	0.87[EUR][1000 genomes]
rs10847869	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12255	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12298151	0.93[ASN][1000 genomes]
rs12298664	0.80[ASN][1000 genomes]
rs12299742	0.80[ASN][1000 genomes]
rs12313006	0.93[ASN][1000 genomes]
rs12314494	0.80[ASN][1000 genomes]
rs12314544	0.80[ASN][1000 genomes]
rs12319654	0.80[ASN][1000 genomes]
rs12369846	0.81[ASN][1000 genomes]
rs12426809	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1532835	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1587856	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671685	0.80[ASN][1000 genomes]
rs1696326	0.80[ASN][1000 genomes]
rs1696349	0.80[ASN][1000 genomes]
rs1799618	0.80[ASN][1000 genomes]
rs1979236	0.80[ASN][1000 genomes]
rs1979237	0.80[ASN][1000 genomes]
rs2061098	1.00[EUR][1000 genomes]
rs2061101	0.92[EUR][1000 genomes]
rs2100500	0.80[ASN][1000 genomes]
rs2135014	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2271049	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2271050	0.88[ASN][1000 genomes]
rs2271051	0.94[ASN][1000 genomes]
rs2292131	0.80[ASN][1000 genomes]
rs2292132	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292134	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292135	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2292136	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2292139	0.93[ASN][1000 genomes]
rs2343108	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2343109	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343685	0.87[EUR][1000 genomes]
rs2649909	0.80[ASN][1000 genomes]
rs2880678	0.87[EUR][1000 genomes]
rs3817094	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825143	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3852536	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3852537	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759355	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4759381	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759382	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759386	0.98[EUR][1000 genomes]
rs4759387	0.98[EUR][1000 genomes]
rs4759389	0.85[EUR][1000 genomes]
rs56272219	0.80[ASN][1000 genomes]
rs59192320	0.94[ASN][1000 genomes]
rs59922385	0.80[ASN][1000 genomes]
rs7138398	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139055	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7303024	0.80[ASN][1000 genomes]
rs73421642	0.80[ASN][1000 genomes]
rs735378	0.80[ASN][1000 genomes]
rs754080	0.80[ASN][1000 genomes]
rs7959441	0.98[EUR][1000 genomes]
rs7972447	1.00[EUR][1000 genomes]
rs7980541	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs897385	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897386	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897391	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897392	0.82[ASN][1000 genomes]
rs897393	0.87[EUR][1000 genomes]
rs921808	0.92[EUR][1000 genomes]
rs936083	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937520	0.80[ASN][1000 genomes]
rs937766	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh 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	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv560490	chr12:123326374-123346971	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv899575	chr12:123326374-123360151	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS 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	11 gene(s)	inside rSNPs	diseases
9	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2292138	CCDC62	cis	Thyroid	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123323200-123340800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:123323600-123340800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:123324600-123344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:123324800-123351600	Weak transcription	Small Intestine	intestine
8	chr12:123326600-123345000	Weak transcription	A549	lung
9	chr12:123327200-123340000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:123327200-123344200	Weak transcription	Hela-S3	cervix
11	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:123329400-123341800	Weak transcription	HepG2	liver
15	chr12:123329600-123344600	Strong transcription	Fetal Intestine Small	intestine
16	chr12:123330000-123340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:123330400-123344400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr12:123330400-123349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:123331000-123340800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:123332200-123341000	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:123332200-123343200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr12:123332600-123341200	Genic enhancers	Brain Cingulate Gyrus	brain
23	chr12:123332600-123344800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:123332600-123355600	Strong transcription	Thymus	Thymus
25	chr12:123333000-123344400	Strong transcription	Spleen	Spleen
26	chr12:123333000-123344600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:123333000-123345000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:123333400-123340800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:123333800-123342800	Weak transcription	Ovary	ovary
30	chr12:123334400-123344400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:123334600-123340200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr12:123334600-123340400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:123335200-123347000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:123335400-123340200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr12:123335600-123342600	Strong transcription	Primary T cells from cord blood	blood
36	chr12:123336000-123342400	Genic enhancers	Brain Inferior Temporal Lobe	brain
37	chr12:123337200-123343400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:123337200-123348800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:123337400-123348400	Weak transcription	HSMM	muscle
40	chr12:123337400-123356200	Weak transcription	Fetal Kidney	kidney
41	chr12:123337600-123340000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:123337600-123341800	Weak transcription	Fetal Lung	lung
43	chr12:123337600-123344200	Weak transcription	Placenta	Placenta
44	chr12:123337600-123344800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:123337600-123348200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:123337600-123351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:123337600-123351400	Weak transcription	HSMMtube	muscle
48	chr12:123337800-123340800	Weak transcription	NHLF	lung
49	chr12:123337800-123341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:123337800-123341800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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