Variant report

Variant	rs10415344
Chromosome Location	chr19:44350718-44350719
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44325529..44327372-chr19:44349912..44351479,2	K562	blood:
2	chr19:44346181..44347972-chr19:44350637..44353162,2	K562	blood:
3	chr19:44342723..44344793-chr19:44350333..44352152,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405318	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10408461	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10412955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10416116	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421861	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10500286	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10500287	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11878787	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11879541	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11880651	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462507	0.93[ASN][1000 genomes]
rs12608578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13344589	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565057	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17712224	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1994414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2016345	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2099356	0.93[ASN][1000 genomes]
rs2163855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2195981	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356401	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356403	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2356432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2356434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239948	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs239949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2883946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs349032	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs4511643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57096959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57133938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59503823	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60036744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60085895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62114569	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118368	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118369	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62118371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62118372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247308	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248807	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7249057	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249413	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs7253002	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253384	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253606	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254659	0.93[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73052639	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73052665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508701	0.95[ASN][1000 genomes]
rs8099861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106802	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112065	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8113286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv458710	chr19:44339960-44410846	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv579853	chr19:44339960-44410846	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10415344	LYPD5	trans	brain	seeQTL
rs10415344	FLJ30469	cis	multi-tissue	Pritchard
rs10415344	KLK8	cis	cerebellum	SCAN
rs10415344	KCNN4	cis	multi-tissue	Pritchard
rs10415344	LYPD5	cis	brain	seeQTL
rs10415344	TBC1D17	cis	parietal	SCAN
rs10415344	DMPK	cis	cerebellum	SCAN
rs10415344	ZNF404	trans	parietal	SCAN
rs10415344	IZUMO2	cis	cerebellum	SCAN
rs10415344	CD3EAP	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44332800-44357200	ZNF genes & repeats	Liver	Liver
2	chr19:44333600-44357400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:44334000-44353200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:44335200-44357200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:44335200-44368200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:44335400-44357200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr19:44335400-44366600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
8	chr19:44336600-44357600	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:44336800-44353000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr19:44336800-44356800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:44336800-44357200	ZNF genes & repeats	Fetal Lung	lung
12	chr19:44338000-44352800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:44339000-44352800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
14	chr19:44339000-44355400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:44339200-44355400	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr19:44339200-44355400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
17	chr19:44339200-44357200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:44339400-44352600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr19:44339400-44352600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
20	chr19:44339400-44355400	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr19:44339400-44355600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:44339600-44355400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
23	chr19:44340800-44353000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:44341000-44352600	ZNF genes & repeats	Fetal Intestine Large	intestine
25	chr19:44341000-44354200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
26	chr19:44341000-44355400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr19:44341000-44357200	ZNF genes & repeats	Brain Anterior Caudate	brain
28	chr19:44341200-44354800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr19:44341200-44357200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:44342000-44353000	ZNF genes & repeats	NH-A	brain
31	chr19:44342200-44355400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
32	chr19:44343000-44352800	ZNF genes & repeats	Fetal Kidney	kidney
33	chr19:44345800-44355400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:44347000-44351400	Weak transcription	Stomach Mucosa	stomach
35	chr19:44347000-44351800	Weak transcription	Fetal Thymus	thymus
36	chr19:44347600-44354600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr19:44347600-44354600	Weak transcription	Fetal Stomach	stomach
38	chr19:44348600-44355400	ZNF genes & repeats	HSMM	muscle
39	chr19:44348600-44357000	ZNF genes & repeats	Fetal Brain Female	brain
40	chr19:44349200-44351400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:44349200-44357200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:44349800-44352600	ZNF genes & repeats	Colonic Mucosa	Colon
43	chr19:44349800-44353000	ZNF genes & repeats	K562	blood
44	chr19:44349800-44354600	ZNF genes & repeats	Fetal Heart	heart
45	chr19:44349800-44355200	ZNF genes & repeats	NHEK	skin
46	chr19:44350000-44354000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr19:44350400-44351000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
48	chr19:44350400-44351000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
49	chr19:44350400-44351000	ZNF genes & repeats	Placenta	Placenta
50	chr19:44350400-44352400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--

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