Variant report

Variant	rs13018466
Chromosome Location	chr2:11317226-11317227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11315684..11318531-chr2:11354814..11356618,2	K562	blood:
2	chr2:11317175..11318147-chr2:11325991..11326847,2	K562	blood:
3	chr2:11294911..11296856-chr2:11315492..11318372,2	K562	blood:
4	chr2:11314637..11317626-chr2:11321207..11322858,2	K562	blood:

Variant related genes	Relation type
ENSG00000162976	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10168084	0.87[CEU][hapmap]
rs10169868	0.90[EUR][1000 genomes]
rs10187981	0.86[CHB][hapmap]
rs10192483	0.80[CEU][hapmap]
rs10495582	0.80[CEU][hapmap]
rs10754958	0.83[CEU][hapmap]
rs10929725	0.81[EUR][1000 genomes]
rs10929727	0.87[CHB][hapmap]
rs10929728	0.86[CHB][hapmap]
rs1129976	0.84[ASN][1000 genomes]
rs11680818	0.80[CEU][hapmap]
rs11891012	0.83[CHB][hapmap]
rs11891877	0.84[ASN][1000 genomes]
rs12470004	0.81[CEU][hapmap]
rs12475086	0.80[CEU][hapmap]
rs12622447	0.86[CHB][hapmap]
rs12987956	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs12996399	0.88[CEU][hapmap];0.96[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13013938	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13022598	0.80[CEU][hapmap]
rs13393192	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13397757	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13404430	0.91[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13423864	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13424069	0.81[CEU][hapmap]
rs1515219	0.84[CEU][hapmap]
rs1546597	0.81[CEU][hapmap]
rs1546598	0.81[CEU][hapmap]
rs17366643	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs17366657	0.81[CEU][hapmap]
rs17366874	0.88[CEU][hapmap]
rs17463896	0.80[CEU][hapmap]
rs1868585	0.86[CHB][hapmap]
rs1901010	0.83[CEU][hapmap]
rs2011812	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2056103	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2122383	0.84[CEU][hapmap]
rs2230774	0.83[EUR][1000 genomes]
rs2271621	0.81[ASN][1000 genomes]
rs2290156	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs3206843	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34727260	0.85[AMR][1000 genomes]
rs36072395	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3732103	0.95[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs3771106	0.84[CEU][hapmap]
rs3856468	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4595944	0.83[EUR][1000 genomes]
rs4669700	0.82[CHB][hapmap]
rs4669702	0.87[CHB][hapmap]
rs4669708	0.86[CHB][hapmap]
rs56243142	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58263533	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62120155	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62120156	0.84[AMR][1000 genomes]
rs6716447	0.84[CEU][hapmap]
rs6728627	0.80[CEU][hapmap]
rs6736194	0.82[CHB][hapmap]
rs6739310	0.83[CHB][hapmap]
rs6743710	0.87[CHB][hapmap]
rs6753921	0.80[CEU][hapmap]
rs726843	0.81[CEU][hapmap]
rs7570428	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7581130	0.83[EUR][1000 genomes]
rs7589152	0.84[CEU][hapmap]
rs7589629	0.80[CEU][hapmap]
rs7598032	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7600696	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8996	0.80[CEU][hapmap]
rs921321	0.86[EUR][1000 genomes]
rs978906	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012083	chr2:11316299-11350604	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	esv3395022	chr2:11316915-11426380	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13018466	PQLC3	cis	Esophagus Muscularis	GTEx
rs13018466	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs13018466	PQLC3	cis	Thyroid	GTEx
rs13018466	PQLC3	cis	lung	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11329400	Weak transcription	Gastric	stomach
2	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
3	chr2:11296400-11318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:11296600-11319200	Weak transcription	Fetal Lung	lung
5	chr2:11296800-11318200	Weak transcription	A549	lung
6	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
7	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
8	chr2:11298200-11317600	Weak transcription	Fetal Brain Male	brain
9	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:11301400-11330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:11301800-11324600	Weak transcription	Primary B cells from cord blood	blood
12	chr2:11302400-11321400	Weak transcription	Fetal Intestine Small	intestine
13	chr2:11302400-11326200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:11302400-11335600	Weak transcription	Lung	lung
15	chr2:11304200-11317800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:11304400-11317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:11304400-11321400	Weak transcription	Esophagus	oesophagus
18	chr2:11304400-11321400	Weak transcription	Fetal Stomach	stomach
19	chr2:11304400-11325200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:11304400-11326400	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:11304400-11329200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:11309800-11318200	Weak transcription	Placenta	Placenta
23	chr2:11309800-11327200	Weak transcription	K562	blood
24	chr2:11309800-11335600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:11310000-11319200	Weak transcription	Adipose Nuclei	Adipose
26	chr2:11310000-11337200	Weak transcription	Ovary	ovary
27	chr2:11310600-11317800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
29	chr2:11312800-11319400	Weak transcription	Fetal Intestine Large	intestine
30	chr2:11313800-11319000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:11314000-11318000	Weak transcription	Fetal Kidney	kidney
32	chr2:11314000-11318400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:11314000-11318400	Weak transcription	HepG2	liver
34	chr2:11314600-11329600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:11314600-11332200	Weak transcription	Colonic Mucosa	Colon
36	chr2:11314600-11364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:11314800-11321400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:11315000-11317400	Enhancers	Dnd41	blood
39	chr2:11315600-11317600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:11315600-11319200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:11315600-11319400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:11315600-11321600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:11315800-11317800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:11315800-11318200	Weak transcription	Brain Angular Gyrus	brain
45	chr2:11315800-11318200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:11315800-11320000	Weak transcription	Left Ventricle	heart
47	chr2:11315800-11321800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:11315800-11322000	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:11315800-11322800	Weak transcription	Fetal Thymus	thymus
50	chr2:11315800-11326400	Weak transcription	Primary T cells fromperipheralblood	blood

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