Variant report

Variant	rs2282492
Chromosome Location	chr11:63918589-63918590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:63898040..63900955-chr11:63917513..63921535,3	K562	blood:
2	chr11:63802623..63804880-chr11:63918427..63921205,3	K562	blood:
3	chr11:63914043..63916614-chr11:63918167..63922101,5	MCF-7	breast:
4	chr11:63916568..63919170-chr11:63931841..63933919,2	MCF-7	breast:
5	chr11:63917406..63919921-chr11:63931137..63933624,2	MCF-7	breast:
6	chr11:63916483..63918216-chr11:63918316..63920658,3	K562	blood:
7	chr11:63918153..63920465-chr11:63921554..63923972,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRPT1-3	chr11:63918390-63918747	NONHSAT021942

No data

Variant related genes	Relation type
ENSG00000133315	Chromatin interaction
ENSG00000256824	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11601522	0.88[ASN][1000 genomes]
rs11603042	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap]
rs11603192	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603384	1.00[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603538	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11604782	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12418535	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12420070	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787945	0.80[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs1860368	0.83[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs2236648	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs2282491	0.92[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2429455	0.85[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs2515241	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2701533	0.80[ASN][1000 genomes]
rs2845597	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3888316	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4980508	0.80[CHB][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap]
rs4980524	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs594942	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs604203	0.85[CHD][hapmap]
rs60452247	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614397	0.88[YRI][hapmap]
rs6591836	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7102177	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7111753	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7112960	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7938819	0.80[CHB][hapmap];0.83[JPT][hapmap]
rs882147	0.80[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	254 gene(s)	inside rSNPs	diseases
3	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
4	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
7	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
8	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
9	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
10	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
11	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
12	esv1801661	chr11:63894054-63937949	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv897663	chr11:63910153-63962152	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	86 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2282492	TRMT112	cis	parietal	SCAN
rs2282492	FAU	cis	parietal	SCAN
rs2282492	TRPT1	cis	Muscle Skeletal	GTEx
rs2282492	PRDX5	cis	parietal	SCAN
rs2282492	MRPL49	cis	cerebellum	SCAN
rs2282492	FKBP2	cis	cerebellum	SCAN
rs2282492	NUDT22	Cis_1M	lymphoblastoid	RTeQTL
rs2282492	PPP1R14B	cis	Muscle Skeletal	GTEx
rs2282492	FKBP2	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63895800-63920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:63900200-63931800	Weak transcription	Lung	lung
3	chr11:63911400-63920200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr11:63911600-63919800	Weak transcription	Primary B cells from cord blood	blood
5	chr11:63911600-63920400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:63911600-63932600	Weak transcription	Primary T cells from cord blood	blood
7	chr11:63911800-63920200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:63914000-63921600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:63914200-63919000	Weak transcription	HepG2	liver
10	chr11:63914200-63920200	Weak transcription	K562	blood
11	chr11:63914400-63920200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:63915200-63918800	Enhancers	Fetal Brain Male	brain
13	chr11:63915400-63919000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:63915400-63919000	Enhancers	Right Ventricle	heart
15	chr11:63915600-63919000	Enhancers	Left Ventricle	heart
16	chr11:63915600-63919000	Enhancers	Psoas Muscle	Psoas
17	chr11:63916000-63918600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:63916000-63920200	Weak transcription	Colonic Mucosa	Colon
19	chr11:63916200-63918600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr11:63916200-63920000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:63916200-63920200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr11:63916200-63920200	Weak transcription	NH-A	brain
23	chr11:63916200-63920400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:63916200-63920400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:63916200-63920400	Weak transcription	A549	lung
26	chr11:63916200-63920800	Enhancers	Liver	Liver
27	chr11:63916200-63921000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:63916200-63924200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:63916200-63932000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:63916400-63918800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:63916400-63919000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr11:63916400-63919000	Enhancers	Fetal Brain Female	brain
33	chr11:63916400-63919800	Strong transcription	Hela-S3	cervix
34	chr11:63916400-63920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:63916400-63920200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr11:63916400-63920400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:63916400-63920400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:63916400-63921400	Enhancers	Brain Germinal Matrix	brain
39	chr11:63916400-63932000	Weak transcription	Stomach Mucosa	stomach
40	chr11:63916600-63918600	Genic enhancers	Fetal Stomach	stomach
41	chr11:63916600-63919200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:63916600-63919400	Genic enhancers	Fetal Muscle Leg	muscle
43	chr11:63916600-63919800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:63916600-63920000	Strong transcription	Fetal Intestine Small	intestine
45	chr11:63916600-63920200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:63916600-63920200	Weak transcription	Fetal Thymus	thymus
47	chr11:63916600-63920200	Weak transcription	Ovary	ovary
48	chr11:63916600-63932200	Weak transcription	Fetal Intestine Large	intestine
49	chr11:63916800-63920400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:63916800-63920800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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