Variant report

Variant	rs11885449
Chromosome Location	chr2:33610911-33610912
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1017677	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.96[ASN][1000 genomes]
rs10198960	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs10495787	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11891105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899010	0.84[JPT][hapmap]
rs13009128	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13385066	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13424241	0.80[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs17012911	0.84[JPT][hapmap]
rs17012917	0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs17012922	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869449	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2015189	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2290426	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2305502	0.88[JPT][hapmap]
rs28414403	0.83[ASN][1000 genomes]
rs28437398	0.83[ASN][1000 genomes]
rs28709139	0.84[ASN][1000 genomes]
rs3769549	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs3769550	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs3820909	0.81[ASN][1000 genomes]
rs58804388	0.97[ASN][1000 genomes]
rs59136259	0.81[ASN][1000 genomes]
rs59877056	0.81[ASN][1000 genomes]
rs6543707	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs6711211	0.84[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6719824	0.83[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7566302	0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1012967	chr2:33533340-33638312	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv535627	chr2:33533340-33638312	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11885449	PTPRK	trans	lymphoblastoid	seeQTL
rs11885449	F13A1	trans	lymphoblastoid	seeQTL
rs11885449	HEY1	trans	lymphoblastoid	seeQTL
rs11885449	SERPINB1	trans	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33578800-33612200	Weak transcription	Fetal Kidney	kidney
2	chr2:33581600-33611400	Weak transcription	Fetal Stomach	stomach
3	chr2:33588400-33624400	Weak transcription	Gastric	stomach
4	chr2:33589200-33623000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr2:33590600-33615800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:33590600-33624800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:33590800-33612600	Weak transcription	Ovary	ovary
8	chr2:33591400-33616000	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:33592000-33624800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:33596200-33614400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:33596400-33613800	Weak transcription	Liver	Liver
12	chr2:33597200-33622200	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:33602200-33613600	Weak transcription	NHLF	lung
14	chr2:33603200-33611200	Weak transcription	Osteobl	bone
15	chr2:33604200-33613000	Weak transcription	NH-A	brain
16	chr2:33604200-33614000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:33604200-33616600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:33604200-33624800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:33604600-33623600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:33604800-33612400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:33604800-33612600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:33604800-33614000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:33604800-33616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:33604800-33616800	Weak transcription	Brain Anterior Caudate	brain
25	chr2:33605400-33616000	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:33606800-33611000	Weak transcription	Fetal Lung	lung
27	chr2:33607400-33611400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:33607600-33616600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:33608200-33614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:33609400-33614200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:33609800-33612600	Weak transcription	Right Ventricle	heart
32	chr2:33609800-33615000	Weak transcription	NHDF-Ad	bronchial
33	chr2:33609800-33630200	Weak transcription	Fetal Heart	heart
34	chr2:33610000-33612600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:33610000-33612800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:33610000-33612800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:33610000-33622200	Weak transcription	Left Ventricle	heart
38	chr2:33610200-33615000	Weak transcription	Psoas Muscle	Psoas
39	chr2:33610400-33612600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr2:33610400-33616200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr2:33610600-33611600	Genic enhancers	Aorta	Aorta
42	chr2:33610600-33614400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:33610800-33611600	Strong transcription	Stomach Smooth Muscle	stomach

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