Variant report

Variant	rs13423864
Chromosome Location	chr2:11347249-11347250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11343484..11345478-chr2:11346697..11348958,2	MCF-7	breast:
2	chr2:11344031..11345866-chr2:11345894..11347764,2	K562	blood:
3	chr2:11343502..11345866-chr2:11345894..11348004,3	K562	blood:
4	chr2:11345703..11347462-chr2:11350332..11352446,3	K562	blood:

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10167277	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10168084	0.85[CEU][hapmap];0.92[AMR][1000 genomes]
rs10169868	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10176416	0.91[AMR][1000 genomes]
rs10180914	0.85[ASN][1000 genomes]
rs10181567	0.98[ASN][1000 genomes]
rs10187981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10189756	0.82[JPT][hapmap]
rs10192483	0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs10204503	0.90[ASN][1000 genomes]
rs10495582	0.82[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes]
rs10754958	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs10929725	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10929726	0.88[AMR][1000 genomes]
rs10929727	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10929728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1129976	0.95[ASN][1000 genomes]
rs11674991	0.87[AMR][1000 genomes]
rs11676201	0.80[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11680818	0.88[CHB][hapmap];0.86[AMR][1000 genomes]
rs11683010	0.92[ASN][1000 genomes]
rs11691429	0.92[AMR][1000 genomes]
rs11891012	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs11891877	0.97[ASN][1000 genomes]
rs12465116	0.90[AMR][1000 genomes]
rs12469980	0.88[ASN][1000 genomes]
rs12470004	0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs12472868	0.89[AMR][1000 genomes]
rs12475086	0.82[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes]
rs12476188	0.83[ASN][1000 genomes]
rs12478098	0.81[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes]
rs12618325	0.94[ASN][1000 genomes]
rs12622447	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12996399	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs13013938	0.86[EUR][1000 genomes]
rs13017010	0.93[ASN][1000 genomes]
rs13018466	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13022598	0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs13030319	0.82[AMR][1000 genomes]
rs13393192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13397757	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13404430	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424069	0.87[CHB][hapmap];0.92[AMR][1000 genomes]
rs1515219	0.85[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes]
rs1546597	0.88[CHB][hapmap];0.92[AMR][1000 genomes]
rs1546598	0.88[CHB][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes]
rs17366643	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17366657	0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs17366874	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs17463896	0.82[CEU][hapmap];0.87[CHB][hapmap];0.89[AMR][1000 genomes]
rs1868585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1901010	0.85[CEU][hapmap];0.87[CHB][hapmap]
rs2011812	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2056103	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2122383	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs2176052	0.86[AMR][1000 genomes]
rs2230774	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2271621	0.94[ASN][1000 genomes]
rs2290156	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2357997	0.87[AMR][1000 genomes]
rs3206843	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34213264	0.89[AMR][1000 genomes]
rs34554628	0.91[ASN][1000 genomes]
rs34586031	0.82[AMR][1000 genomes]
rs34623763	0.82[AMR][1000 genomes]
rs35432367	0.90[AMR][1000 genomes]
rs35508648	0.90[AMR][1000 genomes]
rs35515036	0.90[AMR][1000 genomes]
rs36072395	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732103	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs3771106	0.83[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes]
rs3856468	0.89[CEU][hapmap]
rs4477886	0.83[CHB][hapmap]
rs4595944	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4669700	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4669702	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4669708	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs55641887	0.90[AMR][1000 genomes]
rs55995833	0.89[AMR][1000 genomes]
rs56243142	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56256182	0.89[AMR][1000 genomes]
rs57554471	0.90[AMR][1000 genomes]
rs58263533	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62120155	0.81[EUR][1000 genomes]
rs62121446	0.89[AMR][1000 genomes]
rs62121447	0.89[AMR][1000 genomes]
rs6705170	0.91[JPT][hapmap]
rs6707667	0.80[AMR][1000 genomes]
rs6711793	0.90[AMR][1000 genomes]
rs6716447	0.85[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes]
rs6716817	0.82[CHB][hapmap]
rs6728627	0.88[CHB][hapmap];0.87[AMR][1000 genomes]
rs6736194	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6739310	0.96[CHB][hapmap];1.00[JPT][hapmap]
rs6743710	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6753921	0.82[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes]
rs726843	0.88[CHB][hapmap];0.89[AMR][1000 genomes]
rs7560132	0.87[AMR][1000 genomes]
rs7580593	0.92[AMR][1000 genomes]
rs7581130	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7589152	0.82[CEU][hapmap];0.88[CHB][hapmap];0.90[AMR][1000 genomes]
rs7589629	0.86[AMR][1000 genomes]
rs7598032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7600696	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8996	0.82[CEU][hapmap];0.87[CHB][hapmap];0.86[AMR][1000 genomes]
rs921321	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs921322	0.84[AMR][1000 genomes]
rs978906	0.82[CEU][hapmap];0.87[CHB][hapmap];0.83[YRI][hapmap];0.86[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	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
3	nsv1013570	chr2:11321519-11405246	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13423864	PQLC3	cis	Esophagus Muscularis	GTEx
rs13423864	PQLC3	cis	Thyroid	GTEx
rs13423864	PQLC3	cis	lung	GTEx
rs13423864	ROCK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11296200-11412600	Weak transcription	Aorta	Aorta
2	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
3	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
4	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:11310600-11433000	Weak transcription	Pancreas	Pancrea
6	chr2:11314600-11364200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:11315800-11367400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:11316200-11354200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr2:11316400-11351800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:11318600-11359200	Weak transcription	Fetal Heart	heart
11	chr2:11319000-11364200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:11320800-11377000	Strong transcription	HepG2	liver
13	chr2:11326000-11356600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:11328800-11367600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:11329200-11364400	Strong transcription	Liver	Liver
16	chr2:11329200-11369200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:11330200-11353400	Weak transcription	Gastric	stomach
18	chr2:11332400-11357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:11333400-11347400	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:11333400-11386200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:11333600-11352200	Weak transcription	Psoas Muscle	Psoas
22	chr2:11333800-11353400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:11334400-11363600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:11336200-11354400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:11337000-11367400	Weak transcription	Brain Angular Gyrus	brain
26	chr2:11337400-11350400	Weak transcription	Lung	lung
27	chr2:11337400-11351800	Weak transcription	Fetal Brain Female	brain
28	chr2:11337600-11356400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:11337600-11362600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr2:11338000-11354000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:11338400-11367400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:11338600-11373400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr2:11339600-11351800	Weak transcription	Thymus	Thymus
34	chr2:11339800-11350600	Weak transcription	Fetal Stomach	stomach
35	chr2:11339800-11356200	Weak transcription	Stomach Mucosa	stomach
36	chr2:11339800-11359400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:11339800-11360000	Weak transcription	Spleen	Spleen
38	chr2:11339800-11382600	Weak transcription	Esophagus	oesophagus
39	chr2:11340200-11355000	Weak transcription	Brain Substantia Nigra	brain
40	chr2:11340600-11369400	Weak transcription	Colonic Mucosa	Colon
41	chr2:11340800-11354200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:11340800-11361200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:11341200-11352400	Weak transcription	Brain Anterior Caudate	brain
44	chr2:11341400-11347400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:11341400-11351800	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:11341400-11352000	Weak transcription	Fetal Thymus	thymus
47	chr2:11341400-11353600	Weak transcription	Fetal Brain Male	brain
48	chr2:11341400-11354600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:11341400-11355800	Weak transcription	Brain Germinal Matrix	brain
50	chr2:11341400-11358400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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