Variant report

Variant	rs917567
Chromosome Location	chr17:15442317-15442318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC005838.1-2	chr17:15442295-15442889	ENSG00000263822.1

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10153259	0.89[JPT][hapmap]
rs12450262	0.81[ASN][1000 genomes]
rs12450302	0.81[ASN][1000 genomes]
rs12450921	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12451284	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12938444	0.81[ASN][1000 genomes]
rs12939314	0.89[JPT][hapmap]
rs12943480	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12948266	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12953212	0.81[ASN][1000 genomes]
rs16940991	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17702522	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17702771	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2013835	0.81[ASN][1000 genomes]
rs2532479	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2654261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34236889	0.81[ASN][1000 genomes]
rs34453320	0.81[ASN][1000 genomes]
rs35078459	0.81[ASN][1000 genomes]
rs35406616	0.81[ASN][1000 genomes]
rs35448233	0.81[ASN][1000 genomes]
rs35699886	0.81[ASN][1000 genomes]
rs3852809	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3911955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4054418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4791625	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4792619	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6502459	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6502461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6502462	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs716388	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7226342	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7359507	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7359511	0.83[ASN][1000 genomes]
rs8064461	0.94[ASN][1000 genomes]
rs8068610	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8070714	1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8071082	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8074456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv960418	chr17:15441505-15470653	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs917567	CDRT4	cis	parietal	SCAN
rs917567	TEKT3	cis	parietal	SCAN
rs917567	TEKT3	cis	cerebellum	SCAN
rs917567	CDRT4	cis	cerebellum	SCAN
rs917567	TRIM16	cis	parietal	SCAN
rs917567	SNORD49A	cis	lymphoblastoid	seeQTL
rs917567	FAM18B2	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383400-15455000	Weak transcription	Gastric	stomach
2	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr17:15416200-15466000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:15417600-15466400	Weak transcription	Ovary	ovary
7	chr17:15418600-15450600	Weak transcription	Brain Angular Gyrus	brain
8	chr17:15418800-15450600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr17:15419800-15442400	Weak transcription	Thymus	Thymus
10	chr17:15419800-15448400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr17:15420000-15448400	Weak transcription	Placenta	Placenta
12	chr17:15420000-15450800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr17:15420200-15448600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:15420400-15452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:15420600-15459600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:15420800-15448200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:15420800-15448400	Weak transcription	Fetal Muscle Leg	muscle
18	chr17:15420800-15448400	Weak transcription	HSMM	muscle
19	chr17:15420800-15450200	Weak transcription	Brain Germinal Matrix	brain
20	chr17:15421200-15450800	Weak transcription	Fetal Kidney	kidney
21	chr17:15421200-15453000	Weak transcription	Aorta	Aorta
22	chr17:15421800-15465600	Weak transcription	Hela-S3	cervix
23	chr17:15422400-15447000	Weak transcription	HepG2	liver
24	chr17:15422400-15448400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr17:15422800-15465800	Weak transcription	Fetal Intestine Small	intestine
26	chr17:15423000-15448400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr17:15423000-15451000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:15426200-15446600	Weak transcription	HUVEC	blood vessel
29	chr17:15429200-15442400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:15429200-15443000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr17:15429400-15448400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:15429400-15448400	Weak transcription	Fetal Lung	lung
33	chr17:15429400-15450400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr17:15429800-15448400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:15429800-15450400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr17:15429800-15466000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:15429800-15466400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr17:15430000-15443800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr17:15430200-15448400	Weak transcription	Fetal Intestine Large	intestine
40	chr17:15431000-15465400	Weak transcription	K562	blood
41	chr17:15433000-15449400	Weak transcription	HMEC	breast
42	chr17:15433800-15450600	Weak transcription	Brain Hippocampus Middle	brain
43	chr17:15434600-15448600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr17:15435600-15449200	Weak transcription	Fetal Thymus	thymus
45	chr17:15436200-15448400	Weak transcription	HSMMtube	muscle
46	chr17:15437000-15448400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr17:15437200-15450400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:15438400-15448200	Weak transcription	Liver	Liver
49	chr17:15438800-15450400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr17:15439000-15466000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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