Variant report

Variant	rs205113
Chromosome Location	chr17:19673880-19673881
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs115326	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs118943	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs123081	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs123082	0.84[EUR][1000 genomes]
rs150122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs157387	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157388	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157391	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157392	0.84[EUR][1000 genomes]
rs157393	1.00[CEU][hapmap]
rs157394	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157395	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157396	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157397	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157399	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157400	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157401	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157402	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157403	0.87[EUR][1000 genomes]
rs157405	1.00[CEU][hapmap]
rs157406	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs157408	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs166838	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs166839	0.87[EUR][1000 genomes]
rs169460	0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs169512	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs169513	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs172186	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.84[EUR][1000 genomes]
rs176098	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1812052	0.81[ASN][1000 genomes]
rs1812053	0.81[ASN][1000 genomes]
rs182214	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs184006	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188138	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs192511	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs205087	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs205088	0.95[CHB][hapmap];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs205090	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs205092	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs205093	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205096	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205097	0.97[EUR][1000 genomes]
rs205098	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs205099	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205100	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205103	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs205104	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs205105	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs205106	0.84[EUR][1000 genomes]
rs205107	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205108	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs205110	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs205111	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs205112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385963	0.87[EUR][1000 genomes]
rs281325	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281326	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281327	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281328	0.84[EUR][1000 genomes]
rs281330	0.91[AMR][1000 genomes]
rs281331	0.84[EUR][1000 genomes]
rs281332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281333	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs281334	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs281336	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs281337	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs281338	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs281339	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs281340	0.82[ASN][1000 genomes]
rs281341	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs281342	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs281343	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs281344	0.84[EUR][1000 genomes]
rs281345	0.84[EUR][1000 genomes]
rs281346	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281347	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs281348	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281349	0.84[EUR][1000 genomes]
rs281350	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281352	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281353	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs281354	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281355	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs281356	0.84[EUR][1000 genomes]
rs281365	0.87[EUR][1000 genomes]
rs3098902	0.84[EUR][1000 genomes]
rs3098905	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3098906	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3098907	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3098908	0.84[EUR][1000 genomes]
rs3098909	0.84[EUR][1000 genomes]
rs3101810	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3101811	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3101812	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3101813	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3101814	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs3101815	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34372768	0.87[EUR][1000 genomes]
rs367383	0.87[EUR][1000 genomes]
rs379703	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs383948	0.81[EUR][1000 genomes]
rs383951	0.84[EUR][1000 genomes]
rs395130	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs421561	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs445958	0.81[EUR][1000 genomes]
rs4586510	0.87[EUR][1000 genomes]
rs4924800	0.87[EUR][1000 genomes]
rs4925047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56794428	0.83[ASN][1000 genomes]
rs57944836	0.80[AFR][1000 genomes]
rs59263276	0.85[AFR][1000 genomes]
rs6587203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7213313	0.80[AFR][1000 genomes]
rs7225417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73295824	0.85[AFR][1000 genomes]
rs73295842	0.85[AFR][1000 genomes]
rs73312778	0.85[AFR][1000 genomes]
rs73312783	0.85[AFR][1000 genomes]
rs8066104	0.85[YRI][hapmap]
rs917519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv1063892	chr17:19564634-19808485	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv907866	chr17:19582533-19697976	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv907867	chr17:19603060-19697976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1061489	chr17:19654704-19705026	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv482398	chr17:19673458-19808039	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs205113	ISG20	trans	brain	seeQTL
rs205113	CYP1B1	trans	brain	seeQTL
rs205113	SLC47A1	cis	brain	seeQTL
rs205113	CXCL10	trans	brain	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19657400-19674000	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr17:19664200-19674000	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr17:19666000-19676400	Weak transcription	Fetal Intestine Large	intestine
4	chr17:19666000-19676800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:19666000-19676800	Weak transcription	Fetal Lung	lung
6	chr17:19666000-19677000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:19666000-19678200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr17:19666000-19678600	Weak transcription	Left Ventricle	heart
9	chr17:19666000-19678800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:19666000-19679200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr17:19666000-19691200	Weak transcription	Spleen	Spleen
12	chr17:19666000-19691800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:19666200-19676800	Weak transcription	Gastric	stomach
14	chr17:19666400-19675200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr17:19669600-19674600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr17:19669600-19675000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:19669600-19675000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr17:19669600-19677800	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr17:19670000-19675000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr17:19670200-19674600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr17:19670200-19674800	Weak transcription	Brain Substantia Nigra	brain
22	chr17:19670200-19674800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr17:19670200-19675200	Weak transcription	Right Atrium	heart
24	chr17:19670200-19677000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:19670200-19678400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr17:19670200-19679200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr17:19670200-19679400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:19670200-19694200	Weak transcription	Right Ventricle	heart
29	chr17:19670200-19699400	Weak transcription	Psoas Muscle	Psoas
30	chr17:19670400-19675200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr17:19670400-19678200	Weak transcription	Placenta	Placenta
32	chr17:19670400-19679000	Weak transcription	Colon Smooth Muscle	Colon
33	chr17:19670400-19683800	Weak transcription	Fetal Brain Male	brain
34	chr17:19670600-19674800	Weak transcription	HSMMtube	muscle
35	chr17:19670600-19677200	Weak transcription	Liver	Liver
36	chr17:19670600-19678000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:19670600-19679200	Weak transcription	Pancreas	Pancrea
38	chr17:19670600-19679200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr17:19672000-19676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:19672000-19679000	Weak transcription	Ovary	ovary
41	chr17:19672000-19679200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:19672200-19674400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr17:19672200-19679200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr17:19672600-19674000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr17:19672600-19678800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:19672800-19674000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:19672800-19674200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr17:19672800-19674400	Enhancers	Osteobl	bone
49	chr17:19672800-19674600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr17:19672800-19675000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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