Variant report

Variant	rs10873243
Chromosome Location	chr14:71274579-71274580
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr14:71274546-71277238	Hela-S3	cervix:	n/a	n/a
2	SIN3AK20	chr14:71274569-71277236	MCF-7	breast:	n/a	n/a
3	MAX	chr14:71274553-71277076	MCF-7	breast:	n/a	chr14:71276868-71276877 chr14:71275152-71275162
4	HDAC2	chr14:71274522-71277115	MCF-7	breast:	n/a	chr14:71274540-71274554 chr14:71274699-71274713 chr14:71276765-71276784 chr14:71274698-71274712
5	MTA3	chr14:71274553-71275326	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:71273334..71275325-chr14:71487514..71489742,2	MCF-7	breast:
2	chr14:70233095..70235215-chr14:71274129..71276265,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259153	TF binding region
ENSG00000100650	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10129495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10131177	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10131364	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10134761	0.84[YRI][hapmap]
rs10141804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10143748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10147150	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158882	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11624934	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11625206	0.91[MEX][hapmap];0.87[TSI][hapmap]
rs11625330	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11628333	0.82[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs12886990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12887479	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12888427	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12897648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17108492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1987652	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158530	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158531	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28420983	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35014968	0.81[EUR][1000 genomes]
rs36570	0.85[CHD][hapmap]
rs4899371	0.83[MEX][hapmap]
rs4902843	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4902846	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4902849	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61194329	0.83[EUR][1000 genomes]
rs66736782	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71425216	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71425219	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8019261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8019448	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs8019513	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8020663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8022333	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8022401	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	esv3375447	chr14:71274499-71276497	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10873243	PSEN1	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71222600-71274600	Weak transcription	Hela-S3	cervix
2	chr14:71247800-71274600	Weak transcription	Stomach Mucosa	stomach
3	chr14:71249400-71274600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr14:71249600-71274600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr14:71249800-71274600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr14:71257200-71274600	Weak transcription	Brain Anterior Caudate	brain
7	chr14:71257200-71274600	Weak transcription	Spleen	Spleen
8	chr14:71257800-71274800	Weak transcription	Colonic Mucosa	Colon
9	chr14:71259000-71274600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr14:71260000-71274800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr14:71261200-71274600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr14:71265000-71274600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr14:71265200-71274600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr14:71265800-71274600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr14:71267400-71274600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr14:71267600-71274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr14:71267600-71274600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:71267600-71274600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr14:71267600-71274600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr14:71267600-71274600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr14:71267600-71274600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr14:71267800-71274600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr14:71267800-71274600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:71267800-71274600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr14:71268000-71274600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr14:71268800-71274600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr14:71268800-71274600	Weak transcription	Fetal Intestine Small	intestine
28	chr14:71268800-71274600	Weak transcription	Pancreas	Pancrea
29	chr14:71268800-71275000	Weak transcription	Gastric	stomach
30	chr14:71269200-71274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:71269200-71274800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr14:71269800-71274600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:71270000-71274600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr14:71271000-71274600	Weak transcription	Liver	Liver
35	chr14:71271000-71274600	Weak transcription	Brain Angular Gyrus	brain
36	chr14:71271000-71274600	Weak transcription	Placenta	Placenta
37	chr14:71272000-71274600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr14:71272800-71274600	Enhancers	HepG2	liver
39	chr14:71273000-71280600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr14:71274200-71275000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr14:71274200-71278800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr14:71274200-71279400	Active TSS	HMEC	breast
43	chr14:71274400-71274600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr14:71274400-71274600	Enhancers	Primary B cells from peripheral blood	blood
45	chr14:71274400-71274600	Enhancers	Primary T cells fromperipheralblood	blood
46	chr14:71274400-71274600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:71274400-71274600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr14:71274400-71274600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr14:71274400-71274600	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr14:71274400-71274600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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