Variant report

Variant	rs10771238
Chromosome Location	chr12:9110093-9110094
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHC1-1	chr12:9110019-9111918	refGeneNc_2621_NR_026971

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10129061	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10400516	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10400563	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10743568	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048190	0.82[ASN][1000 genomes]
rs11048195	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs11048264	0.82[ASN][1000 genomes]
rs11048337	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs11048338	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs11048344	0.83[ASN][1000 genomes]
rs11048345	0.83[ASN][1000 genomes]
rs1121401	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11614202	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12423746	0.83[ASN][1000 genomes]
rs12423817	0.83[ASN][1000 genomes]
rs12424026	0.83[ASN][1000 genomes]
rs12812913	0.83[ASN][1000 genomes]
rs12821842	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs12823100	0.96[CHB][hapmap];0.83[ASN][1000 genomes]
rs12833375	0.83[ASN][1000 genomes]
rs1476911	0.91[CHB][hapmap]
rs1805248	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1805724	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs1805725	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805727	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1805732	0.91[CHB][hapmap]
rs1805733	0.91[CHB][hapmap]
rs1805735	0.92[CEU][hapmap];0.96[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1805754	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1805761	0.95[CHB][hapmap]
rs1805765	0.82[CHB][hapmap]
rs2041624	0.83[ASN][1000 genomes]
rs2041625	0.83[ASN][1000 genomes]
rs2284349	0.93[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs2377671	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2377672	0.83[ASN][1000 genomes]
rs2377673	0.83[ASN][1000 genomes]
rs2377674	0.83[ASN][1000 genomes]
rs2377676	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34798934	0.83[ASN][1000 genomes]
rs4309200	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs4639983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883201	0.85[CEU][hapmap]
rs4883203	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832	0.95[CHB][hapmap]
rs7132930	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7300767	0.83[ASN][1000 genomes]
rs7301381	0.81[ASN][1000 genomes]
rs7957321	0.83[ASN][1000 genomes]
rs7961355	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974486	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs887782	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs933462	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs987917	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10771238	M6PR	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9103400-9112000	Weak transcription	Pancreas	Pancrea
2	chr12:9103400-9116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:9103600-9110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:9103600-9114000	Weak transcription	Fetal Kidney	kidney
5	chr12:9103600-9114200	Weak transcription	Aorta	Aorta
6	chr12:9103600-9114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:9103600-9114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:9104000-9110400	Weak transcription	A549	lung
9	chr12:9104000-9111000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:9104000-9113200	Weak transcription	HepG2	liver
11	chr12:9104000-9114400	Weak transcription	Psoas Muscle	Psoas
12	chr12:9104400-9111200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:9104600-9110400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:9104600-9113800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:9105000-9113600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr12:9105000-9113800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:9106600-9116000	Weak transcription	Left Ventricle	heart
18	chr12:9106800-9110600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr12:9106800-9112200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:9106800-9114400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr12:9106800-9114600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr12:9107000-9110200	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:9107000-9111200	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:9107200-9112800	Enhancers	Primary T cells from cord blood	blood
25	chr12:9107200-9112800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:9107400-9112600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:9107400-9112600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:9107400-9112800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:9108600-9115200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:9109000-9110400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:9109000-9111000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:9109000-9111400	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:9109000-9113400	Weak transcription	Right Ventricle	heart
34	chr12:9109000-9114600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:9109000-9115600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:9109000-9121600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:9109400-9112600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:9109400-9113800	Enhancers	Fetal Thymus	thymus
39	chr12:9109600-9110400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:9109600-9114800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:9109800-9110400	Enhancers	Thymus	Thymus
42	chr12:9109800-9110600	Enhancers	K562	blood

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