Variant report

Variant	rs17600375
Chromosome Location	chr15:51345485-51345486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51343342..51345748-chr15:51350368..51352684,2	MCF-7	breast:
2	chr15:51343855..51345742-chr15:51353372..51355019,2	K562	blood:
3	chr15:51333522..51338506-chr15:51338654..51346011,6	MCF-7	breast:
4	chr15:51336930..51339905-chr15:51343675..51346041,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10152338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631696	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631783	0.81[GIH][hapmap]
rs11635474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13380277	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963982	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs17521440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17522120	0.81[GIH][hapmap]
rs17599691	1.00[CHD][hapmap]
rs17600549	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17600569	1.00[ASN][1000 genomes]
rs28552599	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57570932	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57603576	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58449611	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018161	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018162	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018163	0.90[EUR][1000 genomes]
rs62018164	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018166	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018184	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018215	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018216	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018217	1.00[ASN][1000 genomes]
rs62018226	1.00[ASN][1000 genomes]
rs62020176	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020177	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020178	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv428634	chr15:51299632-51446666	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17600375	SPPL2A	Cis_1M	lymphoblastoid	RTeQTL
rs17600375	AP4E1	cis	parietal	SCAN
rs17600375	TRPM7	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51332000-51347000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:51336400-51346800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:51339800-51345800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:51339800-51346800	Weak transcription	Aorta	Aorta
5	chr15:51339800-51348000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:51340000-51347800	Weak transcription	HUVEC	blood vessel
7	chr15:51340200-51346800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:51340200-51352800	Weak transcription	Brain Anterior Caudate	brain
9	chr15:51340400-51349600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:51340600-51346800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:51340600-51348800	Weak transcription	Stomach Mucosa	stomach
12	chr15:51340800-51351800	Weak transcription	Fetal Intestine Small	intestine
13	chr15:51341600-51350800	Weak transcription	HepG2	liver
14	chr15:51341800-51352000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:51342000-51347000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:51343600-51345600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr15:51343600-51346200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:51344400-51346000	Enhancers	Fetal Brain Female	brain
19	chr15:51344600-51346200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:51344600-51346200	Weak transcription	Fetal Brain Male	brain
21	chr15:51344600-51347000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:51344600-51347400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:51344600-51348200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:51344600-51348400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr15:51344600-51349800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:51344600-51352200	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:51344600-51384400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:51344800-51347400	Weak transcription	HSMMtube	muscle
29	chr15:51344800-51348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:51344800-51349600	Weak transcription	Esophagus	oesophagus
31	chr15:51344800-51349600	Weak transcription	Ovary	ovary
32	chr15:51344800-51353600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:51344800-51366800	Weak transcription	Right Ventricle	heart
34	chr15:51345000-51346800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:51345000-51349800	Weak transcription	Right Atrium	heart
36	chr15:51345000-51351200	Strong transcription	HSMM	muscle
37	chr15:51345200-51345800	Enhancers	Fetal Stomach	stomach
38	chr15:51345400-51346600	Weak transcription	Spleen	Spleen
39	chr15:51345400-51349800	Weak transcription	Left Ventricle	heart
40	chr15:51345400-51357000	Weak transcription	Colon Smooth Muscle	Colon

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