Variant report

Variant	rs10425448
Chromosome Location	chr19:20192517-20192518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10405913	1.00[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10409169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415451	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10419563	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421131	0.83[ASN][1000 genomes]
rs10424553	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1080090	0.91[ASN][1000 genomes]
rs11085297	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11882897	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12459967	0.99[ASN][1000 genomes]
rs12461434	1.00[ASN][1000 genomes]
rs2217650	0.94[ASN][1000 genomes]
rs57885738	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58169684	0.88[ASN][1000 genomes]
rs59724513	0.89[ASN][1000 genomes]
rs6511078	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7246986	0.83[CHB][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs7249909	1.00[ASN][1000 genomes]
rs7249965	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250100	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7507883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101545	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8101678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102411	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8109748	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8112652	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking 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	56 gene(s)	inside rSNPs	diseases
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
9	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
10	nsv1062018	chr19:20053658-20193556	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
12	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
14	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
15	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
16	esv3501977	chr19:20072180-20193556	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	esv3501978	chr19:20072180-20193556	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
19	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
20	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
21	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
22	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
23	nsv911322	chr19:20111134-20193556	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
24	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
25	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
26	nsv1057107	chr19:20171392-20193556	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10425448	APLP2	trans	lymphoblastoid	seeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20190000-20192800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr19:20190000-20193000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:20190200-20192600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:20190200-20192800	Weak transcription	Primary T cells from cord blood	blood
5	chr19:20190200-20194000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:20190200-20196200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:20190400-20192600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
8	chr19:20190400-20194800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:20190400-20211400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:20190600-20193400	Weak transcription	Colonic Mucosa	Colon
11	chr19:20190600-20194400	Enhancers	Placenta	Placenta
12	chr19:20190600-20195600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr19:20190800-20192600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:20190800-20193800	Weak transcription	Fetal Muscle Leg	muscle
15	chr19:20190800-20194800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
16	chr19:20190800-20198200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:20191000-20192600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:20191000-20193400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:20191000-20195400	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr19:20191000-20198600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:20191200-20192800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:20191200-20193000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:20191200-20193000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:20191200-20198800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:20191400-20193200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:20191400-20193400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:20191400-20198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:20191800-20192600	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr19:20191800-20192600	Genic enhancers	H9 Cell Line	embryonic stem cell
30	chr19:20191800-20192600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:20191800-20192600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr19:20191800-20192600	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr19:20191800-20192800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
34	chr19:20191800-20192800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:20191800-20193200	ZNF genes & repeats	Fetal Brain Female	brain
36	chr19:20191800-20193600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:20192000-20192800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:20192000-20192800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr19:20192000-20193600	Weak transcription	NHEK	skin
40	chr19:20192000-20194000	Enhancers	Fetal Lung	lung
41	chr19:20192000-20210200	Weak transcription	Ovary	ovary
42	chr19:20192200-20192600	Weak transcription	Fetal Heart	heart
43	chr19:20192200-20192800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:20192200-20194800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:20192400-20192600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr19:20192400-20192600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr19:20192400-20192800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr19:20192400-20193800	Weak transcription	Fetal Stomach	stomach

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