Variant report

Variant	rs17012516
Chromosome Location	chr4:88069143-88069144
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88057518..88060731-chr4:88068893..88070799,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10000784	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10023056	0.82[YRI][hapmap];0.80[AMR][1000 genomes]
rs10025704	0.83[AMR][1000 genomes]
rs10029915	0.82[YRI][hapmap]
rs10032710	0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs1021104	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11946293	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs1481947	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552144	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17012512	0.80[AMR][1000 genomes]
rs17012517	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1842685	0.82[CHD][hapmap];0.89[MEX][hapmap]
rs28505236	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28670747	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28734493	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28882732	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3193672	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3209390	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3733377	0.84[MEX][hapmap]
rs3755980	0.89[MEX][hapmap];1.00[YRI][hapmap]
rs4577539	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs55747890	0.86[AMR][1000 genomes]
rs66477840	0.80[AMR][1000 genomes]
rs66527077	0.84[AMR][1000 genomes]
rs72667790	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7437661	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS 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 target site	27 gene(s)	inside rSNPs	diseases
3	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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 target site	26 gene(s)	inside rSNPs	diseases
4	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1007020	chr4:88046263-88235018	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv537169	chr4:88046263-88235018	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv879526	chr4:88062611-88087832	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17012516	SLC10A6	cis	cerebellum	SCAN
rs17012516	HSD17B13	cis	cerebellar cortex	BrainEAC
rs17012516	HSD17B13	cis	brain	BrainEAC
rs17012516	HSD17B13	cis	cerebellum	SCAN
rs17012516	HSD17B13	cis	multi-tissue	Pritchard
rs17012516	HSD17B13	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88019000-88072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:88042800-88069400	Strong transcription	Placenta	Placenta
3	chr4:88053600-88082000	Weak transcription	HSMM	muscle
4	chr4:88055200-88102800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:88055400-88072200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr4:88055600-88072200	Weak transcription	Fetal Kidney	kidney
7	chr4:88056600-88090600	Weak transcription	Brain Angular Gyrus	brain
8	chr4:88057800-88072600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:88057800-88073800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:88057800-88074000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:88058200-88082400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:88058200-88109000	Weak transcription	Lung	lung
13	chr4:88058400-88074000	Weak transcription	Hela-S3	cervix
14	chr4:88058600-88070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr4:88058600-88071800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:88058600-88084200	Weak transcription	Brain Anterior Caudate	brain
17	chr4:88058800-88069400	Weak transcription	Brain Substantia Nigra	brain
18	chr4:88058800-88073400	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:88058800-88082400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:88058800-88088400	Weak transcription	Thymus	Thymus
21	chr4:88058800-88092200	Weak transcription	Colonic Mucosa	Colon
22	chr4:88059000-88086600	Weak transcription	A549	lung
23	chr4:88059200-88071400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:88059200-88073600	Weak transcription	Pancreas	Pancrea
25	chr4:88059200-88087800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:88059200-88088000	Weak transcription	Fetal Stomach	stomach
27	chr4:88059200-88100800	Weak transcription	Osteobl	bone
28	chr4:88061200-88082200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:88061400-88084000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:88061400-88109400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:88062600-88072200	Weak transcription	NHDF-Ad	bronchial
32	chr4:88062600-88084400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr4:88062800-88070000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:88063000-88069200	Weak transcription	Psoas Muscle	Psoas
35	chr4:88063000-88090800	Weak transcription	Left Ventricle	heart
36	chr4:88063000-88090800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:88063200-88071600	Weak transcription	Fetal Lung	lung
38	chr4:88063200-88088400	Weak transcription	Ovary	ovary
39	chr4:88063200-88097400	Weak transcription	Small Intestine	intestine
40	chr4:88063200-88102000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:88063800-88073800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr4:88063800-88083600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:88063800-88087800	Weak transcription	Primary T cells from cord blood	blood
44	chr4:88064200-88082800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:88064200-88090000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr4:88064200-88098800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:88064200-88100400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:88064400-88071400	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:88064400-88084400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr4:88064400-88092600	Weak transcription	HUVEC	blood vessel

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