Variant report

Variant	rs2888805
Chromosome Location	chr12:104380734-104380735
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSP90B1-3	chr12:104380371-104380803	NONHSAT030404

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10778307	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11111864	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11553765	0.92[AMR][1000 genomes]
rs12426382	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17034946	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17034960	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17035056	0.83[ASN][1000 genomes]
rs17035129	0.92[AMR][1000 genomes]
rs1882019	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2293619	0.81[ASN][1000 genomes]
rs2293626	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2629805	0.94[ASN][1000 genomes]
rs2722200	0.92[ASN][1000 genomes]
rs3751207	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751208	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3829300	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4135060	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4135065	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4135076	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135078	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135082	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4135085	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4135086	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4135087	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4135094	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4135095	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4135118	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4135131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4135150	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55780086	0.95[EUR][1000 genomes]
rs55871448	0.92[AMR][1000 genomes]
rs55893407	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60534873	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73390446	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv3323515	chr12:104379374-104380833	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
4	esv2341266	chr12:104379399-104380904	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region lncRNA miRNA target site	1 gene(s)	inside rSNPs	n/a
5	esv3352410	chr12:104379416-104380846	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
6	esv3396162	chr12:104379427-104380787	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
7	esv9163	chr12:104379439-104380844	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv3367328	chr12:104379622-104382920	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a
9	esv3415317	chr12:104379622-104383320	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104360800-104381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:104361600-104385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:104362000-104382600	Weak transcription	Esophagus	oesophagus
4	chr12:104362000-104384400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:104362000-104392800	Weak transcription	Fetal Brain Male	brain
6	chr12:104362200-104384800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:104363800-104382400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr12:104364000-104381000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:104364600-104383800	Strong transcription	Dnd41	blood
10	chr12:104366600-104383600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:104366800-104381600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:104367600-104381000	Strong transcription	GM12878-XiMat	blood
13	chr12:104368800-104381000	Strong transcription	Primary hematopoietic stem cells	blood
14	chr12:104368800-104381600	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr12:104369200-104381000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:104369200-104381000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr12:104369200-104381000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr12:104369200-104383800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:104369400-104380800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:104369400-104381000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:104369400-104381000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:104369600-104381600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:104369800-104383600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr12:104370000-104381600	Strong transcription	Fetal Thymus	thymus
25	chr12:104370200-104381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:104370200-104381000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:104370200-104381000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:104370200-104384600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:104370400-104380800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:104370400-104381000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:104370400-104381000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:104370400-104381000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:104370400-104381000	Strong transcription	HSMM	muscle
34	chr12:104370400-104381000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr12:104370400-104383600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:104370400-104385000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:104370400-104385600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:104370600-104380800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:104370600-104380800	Strong transcription	HSMMtube	muscle
40	chr12:104370600-104381000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:104370600-104381000	Strong transcription	Duodenum Mucosa	Duodenum
42	chr12:104370600-104381000	Strong transcription	Fetal Intestine Large	intestine
43	chr12:104370600-104381000	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:104370600-104381000	Strong transcription	Placenta	Placenta
45	chr12:104370600-104384000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:104370600-104385000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:104370800-104380800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:104370800-104381000	Strong transcription	Liver	Liver
49	chr12:104370800-104381200	Strong transcription	Adipose Nuclei	Adipose
50	chr12:104370800-104381600	Strong transcription	Fetal Lung	lung

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