Variant report

Variant	rs6716488
Chromosome Location	chr2:233595163-233595164
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHD1-2	chr2:233593258-233595607	NONHSAT077444

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1022329	0.88[EUR][1000 genomes]
rs10427328	0.86[EUR][1000 genomes]
rs1078323	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10933406	0.84[EUR][1000 genomes]
rs1104764	0.82[EUR][1000 genomes]
rs11688166	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11689851	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11893358	0.84[EUR][1000 genomes]
rs12105766	0.87[EUR][1000 genomes]
rs12993791	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999865	0.84[EUR][1000 genomes]
rs13001052	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13021823	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1973675	0.84[EUR][1000 genomes]
rs2293780	0.84[EUR][1000 genomes]
rs2344611	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2344613	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2592104	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs283465	0.87[EUR][1000 genomes]
rs283467	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs283487	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34707169	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35491427	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4144795	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4144797	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62193269	0.81[EUR][1000 genomes]
rs62193271	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704763	0.88[EUR][1000 genomes]
rs6710294	0.87[EUR][1000 genomes]
rs6717048	0.87[EUR][1000 genomes]
rs6733495	0.87[EUR][1000 genomes]
rs6739794	0.86[EUR][1000 genomes]
rs737027	0.84[EUR][1000 genomes]
rs921055	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs974321	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233564200-233596400	Weak transcription	NHLF	lung
2	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
4	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
5	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
6	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
8	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:233569200-233615000	Weak transcription	Colonic Mucosa	Colon
10	chr2:233569400-233612800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:233569400-233615400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:233571200-233598200	Weak transcription	Fetal Kidney	kidney
13	chr2:233571200-233627400	Weak transcription	Gastric	stomach
14	chr2:233571400-233601800	Weak transcription	Esophagus	oesophagus
15	chr2:233571600-233612200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:233580000-233606000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:233580200-233596000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:233580600-233604000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:233580800-233595200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr2:233585600-233595200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:233585800-233604400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:233585800-233626000	Weak transcription	Fetal Heart	heart
24	chr2:233586400-233595800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:233586400-233603200	Strong transcription	Fetal Thymus	thymus
26	chr2:233586400-233612200	Weak transcription	Brain Substantia Nigra	brain
27	chr2:233586800-233599000	Weak transcription	K562	blood
28	chr2:233587000-233630600	Weak transcription	Psoas Muscle	Psoas
29	chr2:233587200-233596600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr2:233587200-233604400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:233587200-233613200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:233588400-233595200	Strong transcription	Fetal Stomach	stomach
33	chr2:233588400-233599600	Strong transcription	Primary T cells from cord blood	blood
34	chr2:233588600-233595600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:233588600-233597000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:233588800-233596400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr2:233588800-233597000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:233588800-233605000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:233589000-233595200	Strong transcription	Brain Germinal Matrix	brain
40	chr2:233589000-233595200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:233589000-233596000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:233589000-233597200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:233589000-233597600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:233589000-233603600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:233589000-233605800	Strong transcription	Liver	Liver
46	chr2:233589200-233596000	Strong transcription	Left Ventricle	heart
47	chr2:233589600-233619800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:233589600-233627000	Weak transcription	Pancreas	Pancrea
49	chr2:233590400-233599200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:233590400-233601600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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