Variant report

Variant	rs1378601
Chromosome Location	chr17:18121926-18121927
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	chr17:18121617..18124692-chr17:18126477..18129347,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131899	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11869205	0.85[ASN][1000 genomes]
rs11870766	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11871970	0.85[ASN][1000 genomes]
rs12150618	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12451754	0.92[ASN][1000 genomes]
rs12936694	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12937300	0.90[CHD][hapmap]
rs12939469	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12939757	0.90[CHD][hapmap]
rs12945597	0.90[CHD][hapmap]
rs12946842	0.83[ASN][1000 genomes]
rs12952556	0.90[CHD][hapmap]
rs1378602	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563631	0.90[CHD][hapmap]
rs1979276	0.90[CHD][hapmap]
rs2245737	0.93[GIH][hapmap];0.84[TSI][hapmap]
rs2273028	0.90[CHD][hapmap]
rs2360234	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2461838	0.90[CHD][hapmap]
rs2605134	0.84[EUR][1000 genomes]
rs2605135	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2605136	0.81[CHD][hapmap]
rs2605142	0.90[CHD][hapmap]
rs2746025	0.90[CHD][hapmap]
rs2746026	0.80[EUR][1000 genomes]
rs2746027	0.90[CHD][hapmap]
rs2746028	0.80[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs2746029	0.80[CEU][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap]
rs28641923	0.90[ASN][1000 genomes]
rs2925137	0.85[ASN][1000 genomes]
rs2925138	0.85[ASN][1000 genomes]
rs3794782	0.96[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4603612	0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4924839	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924840	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4924841	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4925149	0.90[ASN][1000 genomes]
rs4925150	0.90[ASN][1000 genomes]
rs4925171	0.90[CHD][hapmap]
rs56021431	0.85[ASN][1000 genomes]
rs643333	0.90[CHD][hapmap]
rs712270	0.86[JPT][hapmap]
rs712273	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712275	0.81[ASN][1000 genomes]
rs7207123	0.81[CHD][hapmap]
rs7207306	0.90[CHD][hapmap]
rs7212808	0.82[ASN][1000 genomes]
rs7215839	0.90[CHD][hapmap]
rs8069321	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8071834	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854771	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs854772	0.88[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs854775	0.88[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs854776	0.89[EUR][1000 genomes]
rs854779	0.84[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs854781	0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs854795	0.86[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs854798	0.83[ASN][1000 genomes]
rs854801	0.85[ASN][1000 genomes]
rs854804	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs854805	0.83[ASN][1000 genomes]
rs854806	0.83[ASN][1000 genomes]
rs854807	0.83[ASN][1000 genomes]
rs860567	1.00[CHD][hapmap];0.86[JPT][hapmap]
rs860568	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs865923	0.88[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs921986	0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1378601	MYO15A	cis	brain	BrainEAC
rs1378601	LRRC48	cis	parietal	SCAN
rs1378601	MYO15A	cis	cerebellum	SCAN
rs1378601	SHMT1	cis	parietal	SCAN
rs1378601	FLII	cis	cerebellum	SCAN
rs1378601	LOC162632	cis	cerebellum	SCAN
rs1378601	LGALS9C	cis	Whole Blood	GTEx
rs1378601	LOC162632	cis	parietal	SCAN
rs1378601	SHMT1	Cis_1M	lymphoblastoid	RTeQTL
rs1378601	TOP3A	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18109400-18122200	Weak transcription	K562	blood
2	chr17:18110600-18122200	Weak transcription	NHDF-Ad	bronchial
3	chr17:18112600-18127400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:18113000-18128200	Weak transcription	Small Intestine	intestine
5	chr17:18113200-18128200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr17:18113600-18128000	Weak transcription	Colon Smooth Muscle	Colon
7	chr17:18113800-18122000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr17:18113800-18124400	Weak transcription	Hela-S3	cervix
9	chr17:18113800-18124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:18113800-18127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:18113800-18127400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:18113800-18128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:18114200-18122000	Weak transcription	NH-A	brain
14	chr17:18114200-18122200	Weak transcription	Fetal Lung	lung
15	chr17:18114200-18122200	Weak transcription	HUVEC	blood vessel
16	chr17:18114200-18127400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr17:18114200-18127400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:18114200-18127400	Weak transcription	Left Ventricle	heart
19	chr17:18114400-18122200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:18114400-18127400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr17:18114400-18128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:18114600-18122000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:18114600-18122200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:18114600-18122200	Weak transcription	Brain Hippocampus Middle	brain
25	chr17:18114600-18122200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:18114600-18122200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr17:18114600-18122200	Weak transcription	Placenta	Placenta
28	chr17:18114600-18122200	Weak transcription	HSMMtube	muscle
29	chr17:18114600-18122400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr17:18114600-18123800	Weak transcription	GM12878-XiMat	blood
31	chr17:18114600-18124400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr17:18114600-18124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr17:18114600-18124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:18114600-18124400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr17:18114600-18124400	Weak transcription	HMEC	breast
36	chr17:18114600-18124400	Weak transcription	HSMM	muscle
37	chr17:18114600-18124600	Weak transcription	A549	lung
38	chr17:18114600-18127400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:18114600-18127800	Weak transcription	Right Ventricle	heart
40	chr17:18114600-18127800	Weak transcription	Spleen	Spleen
41	chr17:18114600-18128000	Weak transcription	Brain Germinal Matrix	brain
42	chr17:18114600-18128000	Weak transcription	Fetal Brain Female	brain
43	chr17:18114600-18128000	Weak transcription	Lung	lung
44	chr17:18114600-18128000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr17:18114600-18128200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:18114600-18128200	Weak transcription	Liver	Liver
47	chr17:18114600-18128200	Weak transcription	Brain Angular Gyrus	brain
48	chr17:18114600-18128200	Weak transcription	Brain Anterior Caudate	brain
49	chr17:18114600-18128200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr17:18114600-18128200	Weak transcription	Duodenum Mucosa	Duodenum

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