Variant report

Variant	rs1860295
Chromosome Location	chr17:15144868-15144869
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:15139705..15141624-chr17:15144455..15146286,2	K562	blood:
2	chr17:15142573..15145462-chr17:15150924..15153034,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TEKT3-1	chr17:15143744-15147713	ENSG00000265308.1

Variant related genes	Relation type
ENSG00000238806	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13422	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs179520	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192046	0.94[EUR][1000 genomes]
rs230913	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs230914	0.86[EUR][1000 genomes]
rs230931	0.92[EUR][1000 genomes]
rs230934	0.94[EUR][1000 genomes]
rs230935	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230936	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230937	0.94[EUR][1000 genomes]
rs230939	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230941	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs230942	0.93[EUR][1000 genomes]
rs230943	0.94[EUR][1000 genomes]
rs230944	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230946	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230947	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230949	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs230950	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs231030	0.80[ASN][1000 genomes]
rs2531951	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15131600-15145600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr17:15132200-15158800	Weak transcription	Hela-S3	cervix
3	chr17:15134400-15151000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr17:15135800-15151200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr17:15135800-15160200	Weak transcription	Pancreas	Pancrea
6	chr17:15137000-15151200	Weak transcription	Fetal Intestine Small	intestine
7	chr17:15137200-15158000	Weak transcription	Stomach Mucosa	stomach
8	chr17:15139000-15152800	Weak transcription	Colonic Mucosa	Colon
9	chr17:15139800-15148400	Weak transcription	Right Atrium	heart
10	chr17:15139800-15151200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:15139800-15160200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr17:15140000-15145800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:15140200-15147800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr17:15140200-15151000	Weak transcription	HMEC	breast
15	chr17:15142000-15146200	Strong transcription	A549	lung
16	chr17:15142400-15145000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr17:15142600-15145400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr17:15142600-15154000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:15142600-15159000	Weak transcription	Fetal Kidney	kidney
20	chr17:15142600-15159000	Weak transcription	NH-A	brain
21	chr17:15142800-15159200	Weak transcription	Fetal Brain Male	brain
22	chr17:15143000-15145400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr17:15143000-15147800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr17:15143000-15148200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:15143000-15148400	Weak transcription	Spleen	Spleen
26	chr17:15143000-15150800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr17:15143000-15150800	Weak transcription	NHLF	lung
28	chr17:15143000-15151000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr17:15143000-15151200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr17:15143000-15151200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:15143000-15151200	Weak transcription	Osteobl	bone
32	chr17:15143000-15151400	Weak transcription	HUVEC	blood vessel
33	chr17:15143000-15152400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:15143000-15152400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:15143000-15154000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr17:15143000-15156800	Weak transcription	Gastric	stomach
37	chr17:15143200-15146400	Strong transcription	Adipose Nuclei	Adipose
38	chr17:15143200-15147400	Weak transcription	Fetal Lung	lung
39	chr17:15143200-15148400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr17:15143200-15151000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:15143200-15151000	Weak transcription	Fetal Intestine Large	intestine
42	chr17:15143400-15148000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:15143600-15148400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr17:15143800-15145200	Genic enhancers	NHDF-Ad	bronchial
45	chr17:15144000-15150600	Weak transcription	Placenta	Placenta
46	chr17:15144200-15148000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:15144200-15148200	Weak transcription	Brain Substantia Nigra	brain
48	chr17:15144200-15148200	Weak transcription	Fetal Stomach	stomach
49	chr17:15144200-15148400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr17:15144200-15148400	Weak transcription	Left Ventricle	heart

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