Variant report

Variant	rs12467103
Chromosome Location	chr2:11473572-11473573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11294029..11296824-chr2:11471660..11473792,2	K562	blood:
2	chr2:11471245..11477004-chr2:11481417..11486329,8	MCF-7	breast:
3	chr2:11468962..11471644-chr2:11473176..11474699,2	MCF-7	breast:
4	chr2:11472516..11476992-chr2:11482916..11485822,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162976	Chromatin interaction
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10173492	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10929732	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692437	0.84[AMR][1000 genomes]
rs12994807	0.80[AMR][1000 genomes]
rs13016386	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1901011	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2122384	0.80[AMR][1000 genomes]
rs4668721	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4669712	0.84[AMR][1000 genomes]
rs4669713	0.84[AMR][1000 genomes]
rs57404216	1.00[ASN][1000 genomes]
rs58258043	1.00[ASN][1000 genomes]
rs6432185	0.80[AMR][1000 genomes]
rs6736240	0.80[AMR][1000 genomes]
rs6743977	0.89[ASN][1000 genomes]
rs73915164	1.00[ASN][1000 genomes]
rs73915165	1.00[ASN][1000 genomes]
rs73915167	1.00[ASN][1000 genomes]
rs7563468	0.80[AMR][1000 genomes]
rs7575837	0.80[AMR][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	nsv526038	chr2:11369078-11489531	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12467103	PQLC3	Cis_1M	lymphoblastoid	RTeQTL
rs12467103	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11457200-11476400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:11461000-11476400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:11464400-11475200	Weak transcription	Aorta	Aorta
4	chr2:11467000-11480200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:11467400-11481200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:11467600-11481600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:11467800-11480200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:11468000-11476400	Weak transcription	Psoas Muscle	Psoas
9	chr2:11468400-11481200	Weak transcription	HUVEC	blood vessel
10	chr2:11470200-11473800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:11470400-11479800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:11470400-11481400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:11470600-11475200	Weak transcription	Osteobl	bone
14	chr2:11470800-11473600	Weak transcription	K562	blood
15	chr2:11470800-11475000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:11470800-11475200	Weak transcription	NHDF-Ad	bronchial
17	chr2:11470800-11475800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:11470800-11481200	Weak transcription	Right Atrium	heart
19	chr2:11470800-11481800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:11471000-11474800	Weak transcription	Ovary	ovary
21	chr2:11471000-11481200	Weak transcription	HSMM	muscle
22	chr2:11471200-11478600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:11471200-11480400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:11471400-11475800	Enhancers	Liver	Liver
25	chr2:11471600-11477000	Enhancers	HepG2	liver
26	chr2:11472200-11476400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:11472200-11476400	Weak transcription	Pancreas	Pancrea
28	chr2:11472200-11482800	Weak transcription	Gastric	stomach
29	chr2:11472400-11474400	ZNF genes & repeats	A549	lung
30	chr2:11473200-11474200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr2:11473200-11475600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:11473200-11476200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:11473400-11473600	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr2:11473400-11473800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:11473400-11474000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr2:11473400-11474200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:11473400-11474200	Enhancers	Adipose Nuclei	Adipose

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