Variant report

Variant	rs11691429
Chromosome Location	chr2:11342620-11342621
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:11337630..11339492-chr2:11341637..11343755,2	MCF-7	breast:
2	chr2:11334066..11335931-chr2:11342091..11344268,2	MCF-7	breast:
3	chr2:11335303..11337487-chr2:11342422..11345411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134318	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10168084	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10169868	0.91[AMR][1000 genomes]
rs10176416	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10192483	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495582	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929725	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10929726	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11674991	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680818	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465116	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12470004	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12472868	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12475086	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12475627	0.88[ASN][1000 genomes]
rs12478098	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12987956	0.91[EUR][1000 genomes]
rs12996399	0.85[EUR][1000 genomes]
rs12996712	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13022598	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13030319	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13393192	0.92[AMR][1000 genomes]
rs13397757	0.92[AMR][1000 genomes]
rs13404430	0.87[AMR][1000 genomes]
rs13423864	0.92[AMR][1000 genomes]
rs13424069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1515219	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546597	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1546598	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17366643	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17366657	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17366874	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17463896	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2011812	0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2056103	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2122383	0.86[EUR][1000 genomes]
rs2176052	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230774	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2357997	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2358007	0.86[EUR][1000 genomes]
rs3206843	0.87[AMR][1000 genomes]
rs34213264	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34586031	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34623763	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34727260	0.84[EUR][1000 genomes]
rs35407012	0.84[EUR][1000 genomes]
rs35432367	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35508648	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35515036	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35563401	0.88[EUR][1000 genomes]
rs35898907	0.82[EUR][1000 genomes]
rs36072395	0.92[AMR][1000 genomes]
rs3771106	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4477886	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4595944	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55641887	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55995833	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56243142	0.89[AMR][1000 genomes]
rs56256182	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57554471	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58263533	0.88[AMR][1000 genomes]
rs62120156	0.89[EUR][1000 genomes]
rs62121446	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62121447	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6707667	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6711793	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716447	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6716817	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6728627	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6753921	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726843	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7560132	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7580593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581130	0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7589152	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7589629	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7598032	0.92[AMR][1000 genomes]
rs7600696	0.92[AMR][1000 genomes]
rs8996	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs921321	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs921322	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs978906	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	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
rs11691429	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs11691429	PQLC3	cis	Esophagus Muscularis	GTEx
rs11691429	PQLC3	cis	lung	GTEx
rs11691429	PQLC3	cis	Thyroid	GTEx

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	chr2:11316200-11344400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:11316200-11354200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:11316400-11351800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:11318600-11359200	Weak transcription	Fetal Heart	heart
12	chr2:11319000-11364200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:11320800-11377000	Strong transcription	HepG2	liver
14	chr2:11326000-11356600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:11327200-11343400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:11327600-11344400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:11327800-11344200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:11328800-11367600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:11329000-11343200	Strong transcription	NHDF-Ad	bronchial
20	chr2:11329000-11343800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:11329200-11343600	Strong transcription	Dnd41	blood
22	chr2:11329200-11364400	Strong transcription	Liver	Liver
23	chr2:11329200-11369200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:11329400-11343400	Strong transcription	HSMM	muscle
25	chr2:11330200-11353400	Weak transcription	Gastric	stomach
26	chr2:11330400-11343200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:11332400-11357600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr2:11332600-11343200	Strong transcription	Hela-S3	cervix
29	chr2:11333400-11347400	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:11333400-11386200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:11333600-11352200	Weak transcription	Psoas Muscle	Psoas
32	chr2:11333800-11353400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:11334000-11343400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:11334400-11363600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:11334600-11344000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:11334800-11343200	Strong transcription	Placenta	Placenta
37	chr2:11334800-11344000	Strong transcription	Fetal Intestine Large	intestine
38	chr2:11335400-11343200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:11335400-11343400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:11335600-11343200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:11336200-11354400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:11336800-11343400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:11337000-11367400	Weak transcription	Brain Angular Gyrus	brain
44	chr2:11337400-11350400	Weak transcription	Lung	lung
45	chr2:11337400-11351800	Weak transcription	Fetal Brain Female	brain
46	chr2:11337600-11356400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:11337600-11362600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr2:11337800-11347000	Weak transcription	Ovary	ovary
49	chr2:11338000-11354000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:11338400-11347200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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