Variant report

Variant	rs17128370
Chromosome Location	chr14:55748342-55748343
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55748156..55749852-chr14:55763544..55765374,2	K562	blood:
2	chr14:55738364..55741080-chr14:55745206..55748486,4	MCF-7	breast:
3	chr14:55742882..55744479-chr14:55746766..55748710,2	K562	blood:

Variant related genes	Relation type
ENSG00000258469	Chromatin interaction
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10130894	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134937	0.86[EUR][1000 genomes]
rs10135891	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs10138838	0.92[AFR][1000 genomes]
rs10144869	0.88[ASW][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10146943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10149926	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10162552	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10220441	0.82[ASW][hapmap];0.98[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs10498474	1.00[CHB][hapmap]
rs11844441	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11851023	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12323804	0.86[EUR][1000 genomes]
rs13379398	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379420	0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17128159	0.81[GIH][hapmap]
rs17128262	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs17128292	1.00[CHB][hapmap]
rs17128303	1.00[GIH][hapmap];0.83[EUR][1000 genomes]
rs17128323	0.84[AMR][1000 genomes]
rs17128434	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs17128438	0.81[ASW][hapmap];1.00[TSI][hapmap]
rs1886784	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs1952086	0.83[EUR][1000 genomes]
rs2050669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs2065998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs2075598	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs2274272	1.00[CHB][hapmap]
rs2341536	0.86[EUR][1000 genomes]
rs28379450	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661252	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28787988	0.91[ASN][1000 genomes]
rs2880104	0.88[ASN][1000 genomes]
rs28883964	0.82[AMR][1000 genomes]
rs3759666	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs4334208	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61662514	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7147172	0.82[AMR][1000 genomes]
rs7148663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7155704	0.80[AMR][1000 genomes]
rs7155936	1.00[CHB][hapmap]
rs7160575	0.83[EUR][1000 genomes]
rs7161564	1.00[CHB][hapmap]
rs74050958	0.84[AMR][1000 genomes]
rs74050963	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs74050968	1.00[ASN][1000 genomes]
rs74050975	0.86[EUR][1000 genomes]
rs74053904	0.86[EUR][1000 genomes]
rs8007038	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs8009181	1.00[CHB][hapmap]
rs8010853	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8012397	1.00[CHB][hapmap]
rs8016444	0.84[AMR][1000 genomes]
rs8016716	1.00[GIH][hapmap];0.97[MKK][hapmap];0.84[AMR][1000 genomes]
rs8021377	0.86[EUR][1000 genomes]
rs946058	0.86[EUR][1000 genomes]
rs9652341	0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17128370	APP	trans	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55739000-55751400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:55739000-55755600	Weak transcription	Gastric	stomach
3	chr14:55739200-55768400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr14:55740000-55751400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr14:55740000-55751400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:55740000-55770600	Weak transcription	Colonic Mucosa	Colon
7	chr14:55740200-55754200	Weak transcription	Hela-S3	cervix
8	chr14:55740600-55751400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr14:55740800-55750800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:55740800-55751400	Weak transcription	Placenta	Placenta
11	chr14:55740800-55752000	Weak transcription	Esophagus	oesophagus
12	chr14:55741000-55764600	Weak transcription	Fetal Muscle Leg	muscle
13	chr14:55741000-55773200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr14:55741200-55749000	Weak transcription	Right Atrium	heart
15	chr14:55741200-55754000	Weak transcription	Fetal Brain Male	brain
16	chr14:55741800-55750800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr14:55741800-55752400	Weak transcription	A549	lung
18	chr14:55741800-55763800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr14:55741800-55763800	Weak transcription	NHEK	skin
20	chr14:55741800-55764600	Weak transcription	HMEC	breast
21	chr14:55742000-55752200	Weak transcription	Fetal Lung	lung
22	chr14:55742000-55765400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr14:55742200-55749800	Weak transcription	Fetal Kidney	kidney
24	chr14:55742200-55751600	Weak transcription	Osteobl	bone
25	chr14:55742200-55754000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr14:55742200-55754200	Weak transcription	Brain Hippocampus Middle	brain
27	chr14:55742200-55754600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:55742600-55754400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr14:55742800-55752000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr14:55742800-55754200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr14:55744000-55767800	Weak transcription	K562	blood
32	chr14:55744400-55752000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr14:55744800-55748800	Weak transcription	Left Ventricle	heart
34	chr14:55744800-55754600	Weak transcription	HepG2	liver
35	chr14:55744800-55757800	Weak transcription	Fetal Intestine Large	intestine
36	chr14:55744800-55764800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:55744800-55765400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr14:55744800-55767800	Weak transcription	Pancreas	Pancrea
39	chr14:55745000-55749000	Weak transcription	Ovary	ovary
40	chr14:55745000-55752000	Weak transcription	Spleen	Spleen
41	chr14:55745000-55761000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:55745000-55764000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr14:55745000-55768400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr14:55745000-55774000	Weak transcription	Liver	Liver
45	chr14:55745200-55748400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr14:55745200-55751800	Weak transcription	Stomach Mucosa	stomach
47	chr14:55745200-55752200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr14:55745200-55761000	Weak transcription	Thymus	Thymus
49	chr14:55745200-55764000	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr14:55745200-55778400	Weak transcription	Fetal Thymus	thymus

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