Variant report

Variant	rs17400685
Chromosome Location	chr5:96066366-96066367
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96061386..96063186-chr5:96065579..96067865,2	K562	blood:
2	chr5:96055852..96056768-chr5:96066195..96066936,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10447215	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515244	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10515246	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11738135	0.86[EUR][1000 genomes]
rs11739280	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11744642	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11745122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750399	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750400	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11750510	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12186366	0.87[EUR][1000 genomes]
rs12188168	0.85[EUR][1000 genomes]
rs1559085	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17082200	0.86[EUR][1000 genomes]
rs17086588	0.85[CEU][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs17400741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17401901	0.87[EUR][1000 genomes]
rs17402639	0.88[EUR][1000 genomes]
rs17405676	0.89[MEX][hapmap]
rs17478897	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17479052	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34942552	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55695458	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56116814	0.85[EUR][1000 genomes]
rs56122780	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56257788	0.86[EUR][1000 genomes]
rs6864233	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72772090	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72772091	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72772092	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72772095	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72773906	0.87[EUR][1000 genomes]
rs72773912	0.88[EUR][1000 genomes]
rs72773919	1.00[AFR][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	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS 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	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17400685	CAST	cis	cerebellum	SCAN
rs17400685	CAST	cis	multi-tissue	Pritchard
rs17400685	CAST	cis	parietal	SCAN
rs17400685	ERAP1	cis	parietal	SCAN
rs17400685	C5orf36	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
2	chr5:96051000-96067000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr5:96051000-96073600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:96051200-96076800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:96053000-96069600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:96054800-96069600	Weak transcription	Stomach Mucosa	stomach
7	chr5:96054800-96069600	Weak transcription	K562	blood
8	chr5:96054800-96077200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr5:96057000-96067400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:96057600-96067000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:96057800-96075200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:96057800-96076000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:96057800-96098600	Weak transcription	Fetal Brain Male	brain
14	chr5:96058000-96077200	Weak transcription	Small Intestine	intestine
15	chr5:96058000-96078200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:96058200-96067000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr5:96058200-96067600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:96058400-96067000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:96058400-96069800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:96060000-96067000	Strong transcription	Duodenum Mucosa	Duodenum
21	chr5:96060000-96067200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:96060600-96067000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:96060600-96067400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:96060600-96067400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:96061200-96067200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:96061200-96069600	Weak transcription	Right Atrium	heart
27	chr5:96061200-96069800	Weak transcription	Right Ventricle	heart
28	chr5:96061200-96069800	Weak transcription	NHLF	lung
29	chr5:96062000-96067000	Strong transcription	Hela-S3	cervix
30	chr5:96062200-96067000	Strong transcription	Adipose Nuclei	Adipose
31	chr5:96062200-96067000	Strong transcription	Placenta	Placenta
32	chr5:96062200-96067000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:96062200-96070800	Weak transcription	Fetal Lung	lung
34	chr5:96062400-96066800	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:96062400-96067200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr5:96062600-96067200	Strong transcription	Fetal Intestine Large	intestine
37	chr5:96062800-96067400	Strong transcription	Liver	Liver
38	chr5:96062800-96081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
40	chr5:96063600-96066600	Strong transcription	Fetal Intestine Small	intestine
41	chr5:96063600-96066600	Strong transcription	Left Ventricle	heart
42	chr5:96063600-96067000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr5:96063600-96067000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:96063600-96067000	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:96063600-96067200	Strong transcription	Fetal Muscle Trunk	muscle
46	chr5:96063600-96067200	Strong transcription	NH-A	brain
47	chr5:96063800-96067000	Strong transcription	HSMM	muscle
48	chr5:96064200-96069600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:96064600-96067000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr5:96064600-96067200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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