Variant report

Variant	rs172186
Chromosome Location	chr17:19780659-19780660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19766743..19768696-chr17:19780331..19782628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083290	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs115326	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11658169	1.00[LWK][hapmap]
rs118943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs123081	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs123082	0.93[EUR][1000 genomes]
rs150122	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs157387	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs157388	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157389	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157390	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157391	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs157392	0.93[EUR][1000 genomes]
rs157393	1.00[CEU][hapmap]
rs157394	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs157395	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157396	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157397	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs157399	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157400	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157401	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157402	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157403	0.97[EUR][1000 genomes]
rs157405	1.00[CEU][hapmap]
rs157406	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs157407	0.89[GIH][hapmap]
rs157408	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs157409	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs166838	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs166839	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs169460	0.92[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs169512	1.00[CEU][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs169513	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16960550	1.00[LWK][hapmap]
rs176098	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs182214	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184006	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs188138	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs192511	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[EUR][1000 genomes]
rs2010744	1.00[ASW][hapmap]
rs205087	0.80[ASN][1000 genomes]
rs205088	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs205090	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs205092	0.82[ASN][1000 genomes]
rs205093	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205094	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205096	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205097	0.81[EUR][1000 genomes]
rs205098	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs205099	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205100	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205103	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs205104	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs205105	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs205106	0.93[EUR][1000 genomes]
rs205107	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205108	1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs205110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs205111	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[EUR][1000 genomes]
rs205112	0.84[EUR][1000 genomes]
rs205113	0.84[EUR][1000 genomes]
rs2385963	0.97[EUR][1000 genomes]
rs281325	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281326	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281327	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281328	0.93[EUR][1000 genomes]
rs281329	0.83[EUR][1000 genomes]
rs281331	0.93[EUR][1000 genomes]
rs281332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs281333	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs281334	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[EUR][1000 genomes]
rs281336	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs281337	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs281338	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs281339	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs281340	0.95[ASN][1000 genomes]
rs281341	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs281342	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs281343	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs281344	0.93[EUR][1000 genomes]
rs281345	0.93[EUR][1000 genomes]
rs281346	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281347	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs281348	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281349	0.93[EUR][1000 genomes]
rs281350	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281351	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281352	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281353	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs281354	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281355	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs281356	0.93[EUR][1000 genomes]
rs281365	0.97[EUR][1000 genomes]
rs3098902	0.93[EUR][1000 genomes]
rs3098905	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3098906	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3098907	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3098908	0.93[EUR][1000 genomes]
rs3098909	0.93[EUR][1000 genomes]
rs3101810	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs3101811	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3101812	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3101813	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3101814	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs3101815	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34372768	0.97[EUR][1000 genomes]
rs367383	0.97[EUR][1000 genomes]
rs379703	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs383948	0.97[EUR][1000 genomes]
rs383951	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs394008	0.82[AMR][1000 genomes]
rs394009	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs395130	1.00[CEU][hapmap];0.96[GIH][hapmap];0.93[EUR][1000 genomes]
rs421561	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs445958	0.91[EUR][1000 genomes]
rs4586510	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924800	0.97[EUR][1000 genomes]
rs4925043	1.00[ASW][hapmap]
rs4925047	0.84[EUR][1000 genomes]
rs6587203	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7225417	0.84[EUR][1000 genomes]
rs917519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][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	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
4	nsv1057469	chr17:19696714-19787062	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv2763158	chr17:19777544-19789227	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs172186	CXCL10	trans	brain	seeQTL
rs172186	SLC47A1	cis	brain	seeQTL
rs172186	CYP1B1	trans	brain	seeQTL
rs172186	ISG20	trans	brain	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19771600-19787000	Weak transcription	Gastric	stomach
2	chr17:19776000-19782200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr17:19778600-19783200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr17:19778800-19781800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:19778800-19782000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr17:19778800-19782400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:19778800-19783400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr17:19779000-19781200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr17:19779000-19782200	Enhancers	Primary hematopoietic stem cells	blood
10	chr17:19779200-19780800	Enhancers	Primary B cells from cord blood	blood
11	chr17:19779200-19781200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr17:19779200-19781200	Enhancers	Thymus	Thymus
13	chr17:19779800-19780800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr17:19779800-19780800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:19779800-19781200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr17:19780000-19780800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr17:19780000-19780800	Enhancers	Pancreas	Pancrea
18	chr17:19780000-19781000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr17:19780000-19781000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr17:19780200-19781000	Enhancers	Adipose Nuclei	Adipose
21	chr17:19780200-19781000	Enhancers	Dnd41	blood
22	chr17:19780200-19781400	Enhancers	HSMMtube	muscle
23	chr17:19780400-19781000	Enhancers	Fetal Thymus	thymus
24	chr17:19780400-19781800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:19780400-19782400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:19780400-19783200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr17:19780400-19783200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:19780600-19781000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr17:19780600-19781000	Enhancers	Brain Hippocampus Middle	brain
30	chr17:19780600-19783200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr17:19780600-19784200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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