Variant report

Variant	rs17108539
Chromosome Location	chr14:71255435-71255436
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	chr14:71254174..71260054-chr14:71263244..71266960,6	MCF-7	breast:
2	chr14:71253814..71258557-chr14:71260999..71264904,5	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10146964	0.90[CHB][hapmap]
rs11158881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621236	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11622104	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs11622788	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11622989	0.86[CHB][hapmap];0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs11623147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12435875	0.81[ASN][1000 genomes]
rs12437113	0.95[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12437247	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12880887	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap]
rs12897139	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17108533	0.89[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17108537	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17108540	0.94[YRI][hapmap]
rs17108548	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17108555	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1859464	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34509410	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34548271	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34632954	0.84[AFR][1000 genomes]
rs34857523	0.87[AFR][1000 genomes]
rs3829955	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap]
rs67164415	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71425385	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144786	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs7153601	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap]
rs731571	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8014356	0.82[ASN][1000 genomes]
rs8014624	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs8019156	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17108539	SLC8A3	cis	cerebellum	SCAN
rs17108539	ACOT4	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
2	chr14:71222200-71258200	Weak transcription	HepG2	liver
3	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
4	chr14:71223000-71258400	Weak transcription	Primary T cells from cord blood	blood
5	chr14:71223000-71266600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:71224000-71258000	Weak transcription	Dnd41	blood
7	chr14:71227800-71257800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr14:71228000-71258000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr14:71228000-71258000	Weak transcription	A549	lung
10	chr14:71228200-71258000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:71238600-71266600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:71239000-71258000	Weak transcription	Fetal Intestine Small	intestine
13	chr14:71239000-71269600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:71239200-71258200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:71239400-71258200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr14:71239800-71258400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:71240000-71258000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr14:71240200-71257800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:71240600-71255600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr14:71240600-71258000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr14:71242400-71258200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:71242400-71266600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr14:71242600-71266200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr14:71244200-71255800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:71246200-71258000	Weak transcription	Brain Germinal Matrix	brain
26	chr14:71246800-71255800	Weak transcription	Spleen	Spleen
27	chr14:71246800-71266800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr14:71247000-71258200	Weak transcription	Liver	Liver
29	chr14:71247400-71266600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr14:71247600-71256600	Weak transcription	Placenta	Placenta
31	chr14:71247800-71274600	Weak transcription	Stomach Mucosa	stomach
32	chr14:71248200-71258000	Weak transcription	Gastric	stomach
33	chr14:71248200-71258000	Weak transcription	Pancreas	Pancrea
34	chr14:71248200-71271200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:71248800-71257400	Weak transcription	Primary B cells from cord blood	blood
36	chr14:71249000-71266400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr14:71249400-71266200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr14:71249400-71266600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr14:71249400-71266600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr14:71249400-71274400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr14:71249400-71274400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr14:71249400-71274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:71249600-71258600	Weak transcription	GM12878-XiMat	blood
44	chr14:71249600-71274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr14:71249800-71256200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr14:71249800-71274600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr14:71250400-71266600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:71251600-71255600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:71252000-71262800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr14:71252200-71258000	Weak transcription	Fetal Brain Female	brain

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