Variant report

Variant	rs11054701
Chromosome Location	chr12:12289156-12289157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1015830	0.95[ASN][1000 genomes]
rs10743981	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1074992	0.94[CEU][hapmap];0.83[TSI][hapmap]
rs10845498	1.00[CEU][hapmap];0.80[YRI][hapmap];0.80[EUR][1000 genomes]
rs10845504	0.93[CEU][hapmap]
rs11054697	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054752	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1181333	0.82[AFR][1000 genomes]
rs12318846	0.83[AFR][1000 genomes]
rs12580417	0.85[EUR][1000 genomes]
rs1468878	0.80[EUR][1000 genomes]
rs16907786	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16907810	0.92[ASW][hapmap];0.94[CEU][hapmap];0.88[GIH][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2075241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160521	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2160589	0.92[ASW][hapmap];0.93[CEU][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2300231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4265667	0.85[EUR][1000 genomes]
rs4619236	0.92[CEU][hapmap]
rs4763789	0.85[EUR][1000 genomes]
rs61130413	0.84[AFR][1000 genomes]
rs7134001	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7313285	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7968660	0.94[CEU][hapmap]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11054701	CREBL2	cis	lymphoblastoid	seeQTL
rs11054701	DERA	cis	parietal	SCAN
rs11054701	M6PR	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12261600-12301400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
4	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
5	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:12267800-12301600	Weak transcription	NHLF	lung
8	chr12:12268800-12301600	Weak transcription	Brain Substantia Nigra	brain
9	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:12271000-12301600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
12	chr12:12271600-12294200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
14	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:12273600-12301600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
18	chr12:12275000-12303400	Weak transcription	GM12878-XiMat	blood
19	chr12:12276800-12290600	Weak transcription	HSMMtube	muscle
20	chr12:12277400-12306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:12277600-12311600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:12278200-12299200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:12278200-12301400	Weak transcription	Placenta	Placenta
24	chr12:12278200-12310600	Weak transcription	Hela-S3	cervix
25	chr12:12279200-12294200	Weak transcription	Brain Angular Gyrus	brain
26	chr12:12279200-12299000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:12279600-12301400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:12279800-12294000	Weak transcription	Brain Anterior Caudate	brain
29	chr12:12279800-12300000	Weak transcription	HUVEC	blood vessel
30	chr12:12279800-12303600	Weak transcription	Fetal Brain Male	brain
31	chr12:12279800-12311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:12279800-12311000	Weak transcription	HMEC	breast
33	chr12:12279800-12311600	Weak transcription	Dnd41	blood
34	chr12:12279800-12313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:12279800-12342800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:12280000-12290600	Weak transcription	Ovary	ovary
37	chr12:12280000-12291600	Weak transcription	NHEK	skin
38	chr12:12280000-12299200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr12:12280000-12301600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr12:12280000-12301600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:12280000-12302600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr12:12280000-12303400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:12280400-12299600	Weak transcription	Osteobl	bone
44	chr12:12280600-12300000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:12280600-12301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:12281400-12301600	Weak transcription	Left Ventricle	heart
47	chr12:12281800-12335600	Weak transcription	Psoas Muscle	Psoas
48	chr12:12282400-12298800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:12282400-12299000	Weak transcription	Adipose Nuclei	Adipose
50	chr12:12282400-12299200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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