Variant report

Variant	rs12412095
Chromosome Location	chr10:6113523-6113524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL2RA-4	chr10:6113477-6113881	NONHSAT011204

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10905713	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10905718	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10905719	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11256593	0.87[ASN][1000 genomes]
rs11256601	0.84[ASN][1000 genomes]
rs2182410	0.82[ASN][1000 genomes]
rs3118469	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118470	0.86[ASW][hapmap];0.86[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs3118471	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3134883	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147359	0.92[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4749955	0.95[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs7078535	0.84[ASN][1000 genomes]
rs7907829	0.85[EUR][1000 genomes]
rs9633775	0.81[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	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv894815	chr10:6108439-6161781	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12412095	PFKP	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6104600-6113600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr10:6106800-6114800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr10:6107200-6114800	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr10:6107200-6115000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr10:6107400-6114800	Enhancers	Primary hematopoietic stem cells	blood
6	chr10:6108000-6115600	Enhancers	Primary B cells from peripheral blood	blood
7	chr10:6108800-6113600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr10:6108800-6114200	Weak transcription	Right Ventricle	heart
9	chr10:6109400-6115400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:6109400-6117400	Enhancers	Fetal Thymus	thymus
11	chr10:6111000-6113800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:6111000-6114600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr10:6111000-6115000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr10:6111200-6113600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:6111200-6114800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr10:6111200-6115000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr10:6111200-6115000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr10:6111400-6114200	Enhancers	Thymus	Thymus
19	chr10:6111400-6115200	Enhancers	Primary B cells from cord blood	blood
20	chr10:6111600-6114400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr10:6111600-6115000	Enhancers	Primary T cells from cord blood	blood
22	chr10:6111600-6115000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr10:6111600-6115200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr10:6111600-6115200	Enhancers	Dnd41	blood
25	chr10:6112200-6114400	Enhancers	Lung	lung
26	chr10:6112200-6114800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr10:6112400-6113600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr10:6112400-6113600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr10:6112400-6113800	Enhancers	GM12878-XiMat	blood
30	chr10:6112400-6114600	Enhancers	Adipose Nuclei	Adipose
31	chr10:6112400-6114800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr10:6112600-6113800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr10:6112600-6114000	Enhancers	Placenta	Placenta
34	chr10:6112600-6114400	Enhancers	Spleen	Spleen
35	chr10:6112800-6114000	Enhancers	Brain Anterior Caudate	brain
36	chr10:6112800-6114400	Enhancers	Left Ventricle	heart
37	chr10:6113000-6113800	Enhancers	Brain Hippocampus Middle	brain
38	chr10:6113000-6115000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr10:6113000-6115200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr10:6113200-6113600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr10:6113200-6113600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr10:6113400-6113600	Enhancers	Fetal Muscle Leg	muscle
43	chr10:6113400-6113800	Enhancers	Small Intestine	intestine
44	chr10:6113400-6114000	Enhancers	Right Atrium	heart
45	chr10:6113400-6114600	Enhancers	Primary T helper cells PMA-I stimulated	--

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