Variant report

Variant	rs10027456
Chromosome Location	chr4:16258163-16258164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD38-2	chr4:16257880-16259810	ENSG00000225917
2	lnc-CD38-2	chr4:16257931-16258367	ENSG00000263327.1
3	lnc-CD38-2	chr4:16257880-16259810	ENSG00000263327.1
4	lnc-CD38-2	chr4:16257931-16259810	NONHSAT095674
5	lnc-CD38-2	chr4:16257880-16258303	NONHSAT095679

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10025014	0.82[ASN][1000 genomes]
rs10212713	0.82[ASN][1000 genomes]
rs12502431	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs203438	0.82[ASN][1000 genomes]
rs2109889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34159213	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73802022	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16229800-16259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:16234200-16264800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:16234400-16261600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:16235400-16272800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:16235600-16261600	Weak transcription	Fetal Kidney	kidney
6	chr4:16238200-16258800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:16238200-16266000	Weak transcription	Fetal Brain Male	brain
8	chr4:16238400-16258400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:16240000-16259800	Weak transcription	Fetal Lung	lung
10	chr4:16240400-16263400	Weak transcription	Fetal Thymus	thymus
11	chr4:16242200-16267800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:16243400-16259200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:16244000-16265000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:16244200-16258200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr4:16245000-16261200	Weak transcription	Spleen	Spleen
16	chr4:16245600-16266000	Weak transcription	Brain Angular Gyrus	brain
17	chr4:16246000-16261400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:16246400-16259200	Weak transcription	Thymus	Thymus
19	chr4:16249600-16261200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:16251000-16259200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:16251000-16260000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:16251800-16264400	Weak transcription	Fetal Brain Female	brain
23	chr4:16252000-16260400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:16252800-16259600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr4:16252800-16266600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:16252800-16267400	Weak transcription	Pancreas	Pancrea
27	chr4:16253600-16259600	Strong transcription	Primary B cells from cord blood	blood
28	chr4:16254800-16268800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr4:16255000-16258200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:16255200-16259600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:16255200-16261000	Weak transcription	Brain Anterior Caudate	brain
32	chr4:16255800-16258800	Weak transcription	HepG2	liver
33	chr4:16256000-16259000	Weak transcription	Hela-S3	cervix
34	chr4:16256200-16259600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:16256200-16260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:16256200-16261200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:16256200-16261600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:16256200-16270800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:16256400-16259200	Weak transcription	NHDF-Ad	bronchial
40	chr4:16256400-16261400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:16256400-16266400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:16256400-16270600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr4:16256600-16260800	Weak transcription	NHLF	lung
44	chr4:16257200-16258800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
45	chr4:16257200-16258800	Strong transcription	Fetal Stomach	stomach
46	chr4:16257200-16259400	Strong transcription	Fetal Muscle Leg	muscle
47	chr4:16257400-16258200	Strong transcription	Liver	Liver
48	chr4:16257400-16258600	Strong transcription	Brain Hippocampus Middle	brain
49	chr4:16257400-16258600	Strong transcription	Left Ventricle	heart
50	chr4:16257400-16259200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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