Variant report

Variant	rs12052613
Chromosome Location	chr2:55478226-55478227
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	chr2:55477304..55482522-chr2:55492330..55496996,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10200120	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1056445	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11357	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12988617	0.85[ASN][1000 genomes]
rs17852670	0.80[ASN][1000 genomes]
rs2576708	0.82[AFR][1000 genomes]
rs2576711	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2576712	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576719	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2576721	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2589080	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2589092	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2589093	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589094	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589096	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2589100	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864819	0.90[ASN][1000 genomes]
rs2864826	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2917779	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920967	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34348115	0.85[ASN][1000 genomes]
rs34511570	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4435493	0.81[ASN][1000 genomes]
rs55997390	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56039135	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6545480	0.94[ASN][1000 genomes]
rs6706815	0.81[ASN][1000 genomes]
rs6755515	0.85[ASN][1000 genomes]
rs72799507	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7580936	0.80[EUR][1000 genomes]
rs7597293	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12052613	LOC388720///RPS27A	Cis_1M	lymphoblastoid	RTeQTL
rs12052613	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL
rs12052613	CLHC1	cis	Artery Tibial	GTEx
rs12052613	CLHC1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55461600-55481600	Strong transcription	Fetal Thymus	thymus
2	chr2:55461600-55495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55461600-55495400	Weak transcription	Stomach Mucosa	stomach
4	chr2:55461800-55493400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:55461800-55495000	Weak transcription	Fetal Brain Male	brain
6	chr2:55462000-55493200	Strong transcription	Duodenum Mucosa	Duodenum
7	chr2:55462200-55490200	Weak transcription	Small Intestine	intestine
8	chr2:55462600-55485800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:55463000-55480200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:55463000-55481000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:55463000-55495400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:55463200-55481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:55463400-55488200	Weak transcription	Pancreas	Pancrea
14	chr2:55463600-55483800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:55463800-55479600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:55463800-55486200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:55463800-55490400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:55463800-55494800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:55463800-55495600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55464400-55479600	Weak transcription	NHLF	lung
21	chr2:55464600-55479400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:55464600-55495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:55465400-55490600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:55465600-55486000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:55465600-55494400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:55466000-55493200	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:55468200-55493400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:55468400-55493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:55468400-55494400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:55468600-55494400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:55468800-55480400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:55468800-55493600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:55468800-55494400	Strong transcription	Adipose Nuclei	Adipose
34	chr2:55468800-55494400	Strong transcription	Liver	Liver
35	chr2:55469000-55482000	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:55469400-55492600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:55469600-55481400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:55469600-55481800	Strong transcription	Placenta	Placenta
39	chr2:55469800-55478600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:55470000-55481800	Strong transcription	A549	lung
41	chr2:55470800-55494200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:55471000-55479400	Weak transcription	Brain Substantia Nigra	brain
43	chr2:55471600-55478600	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:55472000-55485000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:55472000-55495200	Weak transcription	Psoas Muscle	Psoas
46	chr2:55472800-55479400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:55472800-55479400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:55473000-55482400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:55473600-55481400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:55473600-55484600	Weak transcription	Hela-S3	cervix

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