Variant report

Variant	rs11676250
Chromosome Location	chr2:33707734-33707735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LTBP1-1	chr2:33706250-33708003	NONHSAT070011

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10495789	0.84[CEU][hapmap];0.89[JPT][hapmap]
rs13009794	0.84[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1378725	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17013126	1.00[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34432178	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34530057	0.86[ASN][1000 genomes]
rs35582579	0.84[ASN][1000 genomes]
rs35799810	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57647413	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61382538	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543716	0.83[CHD][hapmap]
rs6716035	0.91[EUR][1000 genomes]
rs6736350	0.92[CEU][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741198	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6757351	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6758071	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6758325	0.88[CHD][hapmap]
rs719546	0.89[JPT][hapmap]
rs765253	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.98[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	nsv873792	chr2:33682737-33715742	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1829750	chr2:33704194-33740571	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33703200-33708600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:33703200-33709200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:33703600-33708800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:33703600-33711800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:33703600-33715600	Weak transcription	Spleen	Spleen
6	chr2:33704600-33707800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:33704800-33717600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:33705000-33708600	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr2:33705000-33710800	Enhancers	Fetal Heart	heart
10	chr2:33705000-33714000	Weak transcription	Right Ventricle	heart
11	chr2:33705200-33709400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:33705600-33709600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:33705600-33710000	Weak transcription	Pancreas	Pancrea
14	chr2:33705800-33709000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:33705800-33709200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:33705800-33709600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:33706000-33708600	Weak transcription	Psoas Muscle	Psoas
18	chr2:33706000-33709200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:33706000-33714400	Weak transcription	Right Atrium	heart
20	chr2:33706200-33709200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:33706400-33707800	Weak transcription	Primary B cells from cord blood	blood
22	chr2:33707400-33707800	Enhancers	Brain Anterior Caudate	brain
23	chr2:33707400-33707800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
24	chr2:33707400-33707800	Enhancers	HSMMtube	muscle
25	chr2:33707400-33708000	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:33707400-33708000	Enhancers	Brain Hippocampus Middle	brain
27	chr2:33707400-33708000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr2:33707400-33708200	Enhancers	Brain Substantia Nigra	brain
29	chr2:33707400-33708200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr2:33707400-33710600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr2:33707600-33708000	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr2:33707600-33708200	Enhancers	NHDF-Ad	bronchial
33	chr2:33707600-33708600	Weak transcription	Left Ventricle	heart
34	chr2:33707600-33709000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:33707600-33709200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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