Variant report

Variant	rs17688725
Chromosome Location	chr14:56604840-56604841
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	chr14:56602302..56604892-chr14:56607961..56609487,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10144612	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10483656	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1427556	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap]
rs17688801	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17689278	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17761563	1.00[CHD][hapmap];0.81[GIH][hapmap]
rs17762499	0.90[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17762733	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17832675	0.81[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1951955	1.00[CEU][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2035283	0.91[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2343376	0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28712711	0.82[EUR][1000 genomes]
rs2880615	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3850298	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3912203	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4127813	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8020301	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533129	chr14:56568535-56819234	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1844788	chr14:56594420-56771207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17688725	C14orf166	cis	cerebellum	SCAN
rs17688725	PSMC6	cis	cerebellum	SCAN
rs17688725	C14orf37	cis	cerebellum	SCAN
rs17688725	ARID4A	cis	cerebellum	SCAN
rs17688725	ERO1L	cis	parietal	SCAN
rs17688725	MAPK1IP1L	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56593200-56612800	Weak transcription	Brain Angular Gyrus	brain
2	chr14:56595600-56607000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr14:56596600-56615000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:56597000-56611800	Weak transcription	Lung	lung
5	chr14:56597200-56605600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr14:56597200-56607200	Enhancers	Dnd41	blood
7	chr14:56598200-56606600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:56599200-56606600	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr14:56599400-56614800	Weak transcription	Brain Substantia Nigra	brain
10	chr14:56599400-56615000	Weak transcription	Left Ventricle	heart
11	chr14:56599600-56605600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr14:56600000-56607800	Enhancers	Primary hematopoietic stem cells	blood
13	chr14:56600400-56605400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:56600400-56606800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:56600600-56605800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr14:56600600-56605800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr14:56600600-56608400	Weak transcription	Gastric	stomach
18	chr14:56600600-56615000	Weak transcription	Right Atrium	heart
19	chr14:56601000-56607800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr14:56601200-56606000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr14:56601800-56605000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr14:56603000-56607000	Enhancers	Fetal Brain Male	brain
23	chr14:56603400-56605000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr14:56603400-56605000	Enhancers	Primary B cells from cord blood	blood
25	chr14:56603400-56606000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr14:56603400-56606000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr14:56603400-56606000	Enhancers	Ovary	ovary
28	chr14:56603400-56607600	Enhancers	Fetal Brain Female	brain
29	chr14:56603600-56606000	Enhancers	Pancreas	Pancrea
30	chr14:56603600-56606400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr14:56603600-56607400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr14:56603800-56605600	Weak transcription	Spleen	Spleen
33	chr14:56603800-56607000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr14:56604000-56606000	Enhancers	H1 Cell Line	embryonic stem cell
35	chr14:56604000-56606000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:56604000-56606000	Enhancers	Fetal Thymus	thymus
37	chr14:56604000-56610400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr14:56604200-56606000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:56604200-56606000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr14:56604200-56614800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr14:56604400-56605400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:56604400-56605600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr14:56604400-56608400	Weak transcription	Stomach Mucosa	stomach
44	chr14:56604400-56610800	Weak transcription	Colon Smooth Muscle	Colon
45	chr14:56604600-56605000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr14:56604600-56605000	Enhancers	Brain Anterior Caudate	brain
47	chr14:56604600-56605000	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr14:56604600-56605000	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr14:56604600-56605600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr14:56604600-56606200	Enhancers	Thymus	Thymus

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