Variant report

Variant	rs12996399
Chromosome Location	chr2:11313839-11313840
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	chr2:11293678..11297102-chr2:11313407..11316092,5	MCF-7	breast:
2	chr2:11313501..11315110-chr2:11621698..11623847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162976	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10168084	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs10176416	0.82[EUR][1000 genomes]
rs10187981	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10192483	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10495582	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10754958	0.88[CEU][hapmap]
rs10929726	0.85[EUR][1000 genomes]
rs10929727	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10929728	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1129976	0.84[ASN][1000 genomes]
rs11674991	0.83[EUR][1000 genomes]
rs11680818	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11691429	0.85[EUR][1000 genomes]
rs11891012	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs11891877	0.83[ASN][1000 genomes]
rs12465116	0.84[EUR][1000 genomes]
rs12470004	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs12472868	0.81[EUR][1000 genomes]
rs12475086	0.92[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs12478098	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs12622447	0.91[CHB][hapmap]
rs12987956	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13013938	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13018466	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]
rs13022598	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs13393192	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs13397757	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs13404430	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs13423864	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs13424069	0.93[CEU][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs1515219	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1546597	0.93[CEU][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs1546598	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs17366643	0.81[YRI][hapmap]
rs17366657	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs17366874	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs17463896	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs1868585	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1901010	0.88[CEU][hapmap]
rs2011812	0.81[YRI][hapmap]
rs2122383	0.89[CEU][hapmap]
rs2271621	0.80[ASN][1000 genomes]
rs2290156	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs2357997	0.83[EUR][1000 genomes]
rs3206843	0.80[ASN][1000 genomes]
rs34213264	0.81[EUR][1000 genomes]
rs34727260	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35432367	0.83[EUR][1000 genomes]
rs35508648	0.80[EUR][1000 genomes]
rs35515036	0.81[EUR][1000 genomes]
rs35563401	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35898907	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36072395	0.80[ASN][1000 genomes]
rs3732103	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771106	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs3856468	0.82[AMR][1000 genomes]
rs3951242	0.82[AMR][1000 genomes]
rs4669700	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4669702	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4669708	0.91[CHB][hapmap]
rs55641887	0.84[EUR][1000 genomes]
rs55995833	0.84[EUR][1000 genomes]
rs56243142	0.83[ASN][1000 genomes]
rs56256182	0.82[EUR][1000 genomes]
rs57554471	0.82[EUR][1000 genomes]
rs58263533	0.82[ASN][1000 genomes]
rs62120155	0.84[AMR][1000 genomes]
rs62120156	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62121446	0.83[EUR][1000 genomes]
rs62121447	0.83[EUR][1000 genomes]
rs6711793	0.85[EUR][1000 genomes]
rs6716447	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6728627	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6736194	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6739310	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs6743710	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6753921	0.92[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs726843	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs7560132	0.84[EUR][1000 genomes]
rs7570428	0.82[AMR][1000 genomes]
rs7580593	0.85[EUR][1000 genomes]
rs7589152	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7589629	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7598032	0.81[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap]
rs8996	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs921322	0.87[EUR][1000 genomes]
rs978906	0.92[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12996399	PQLC3	cis	lung	GTEx
rs12996399	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs12996399	PQLC3	cis	Thyroid	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

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	chr2:11296400-11314200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:11296400-11314800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:11296400-11315200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:11296400-11315200	Weak transcription	Brain Substantia Nigra	brain
7	chr2:11296400-11315400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:11296400-11318800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:11296600-11315200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:11296600-11315200	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:11296600-11315200	Weak transcription	NHDF-Ad	bronchial
12	chr2:11296600-11319200	Weak transcription	Fetal Lung	lung
13	chr2:11296800-11315000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:11296800-11315200	Weak transcription	Brain Anterior Caudate	brain
15	chr2:11296800-11318200	Weak transcription	A549	lung
16	chr2:11296800-11379800	Weak transcription	Small Intestine	intestine
17	chr2:11297600-11315200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:11297600-11394400	Weak transcription	Right Ventricle	heart
19	chr2:11297800-11315200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:11298200-11315400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:11298200-11317600	Weak transcription	Fetal Brain Male	brain
22	chr2:11299200-11357000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:11300200-11315400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:11300600-11315400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr2:11301400-11330400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr2:11301600-11315200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:11301800-11315400	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:11301800-11324600	Weak transcription	Primary B cells from cord blood	blood
29	chr2:11302000-11315200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:11302400-11315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:11302400-11315400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:11302400-11321400	Weak transcription	Fetal Intestine Small	intestine
33	chr2:11302400-11326200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:11302400-11335600	Weak transcription	Lung	lung
35	chr2:11303800-11314600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr2:11304200-11315200	Weak transcription	Primary T cells from cord blood	blood
37	chr2:11304200-11317800	Weak transcription	Fetal Muscle Leg	muscle
38	chr2:11304400-11314400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:11304400-11315200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:11304400-11315200	Weak transcription	HMEC	breast
41	chr2:11304400-11315200	Weak transcription	HSMM	muscle
42	chr2:11304400-11315400	Weak transcription	Left Ventricle	heart
43	chr2:11304400-11315400	Weak transcription	HSMMtube	muscle
44	chr2:11304400-11317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:11304400-11321400	Weak transcription	Esophagus	oesophagus
46	chr2:11304400-11321400	Weak transcription	Fetal Stomach	stomach
47	chr2:11304400-11325200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:11304400-11326400	Weak transcription	Colon Smooth Muscle	Colon
49	chr2:11304400-11329200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:11304800-11315400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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