Variant report

Variant	rs11620816
Chromosome Location	chr14:31619392-31619393
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11622403	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs11624437	0.92[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap]
rs11625570	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs11625798	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11626343	0.96[EUR][1000 genomes]
rs11845860	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11848094	0.93[EUR][1000 genomes]
rs11848563	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17097688	0.92[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs17097735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17097741	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17097743	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs34039100	0.86[EUR][1000 genomes]
rs34684806	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34745649	0.96[EUR][1000 genomes]
rs3825741	0.82[GIH][hapmap]
rs3954287	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs45610935	0.87[EUR][1000 genomes]
rs4981818	0.82[GIH][hapmap]
rs55907561	0.82[EUR][1000 genomes]
rs56168081	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56346233	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57000706	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57893693	0.96[EUR][1000 genomes]
rs58071351	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58204331	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58771204	0.87[EUR][1000 genomes]
rs59458716	0.96[EUR][1000 genomes]
rs59933112	0.94[EUR][1000 genomes]
rs60350855	0.94[EUR][1000 genomes]
rs60928004	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61592116	0.94[EUR][1000 genomes]
rs6571389	0.81[GIH][hapmap]
rs66528205	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67960414	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7155228	0.82[GIH][hapmap]
rs72670334	0.84[EUR][1000 genomes]
rs72670351	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72670364	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72670371	0.96[EUR][1000 genomes]
rs72670374	0.96[EUR][1000 genomes]
rs72670375	0.96[EUR][1000 genomes]
rs72670377	0.96[EUR][1000 genomes]
rs72670385	0.96[EUR][1000 genomes]
rs72670390	0.96[EUR][1000 genomes]
rs72670391	0.96[EUR][1000 genomes]
rs72670396	0.96[EUR][1000 genomes]
rs72670398	0.93[EUR][1000 genomes]
rs72670399	0.96[EUR][1000 genomes]
rs8021054	0.82[GIH][hapmap]
rs9888564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048736	chr14:31447842-31624912	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1049063	chr14:31473521-31622741	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv901587	chr14:31501505-31752664	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv832763	chr14:31501597-31680021	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv1050054	chr14:31501703-31733642	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases
6	nsv1043033	chr14:31538984-31686696	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv901588	chr14:31595666-31639111	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3345810	chr14:31599017-31622767	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11620816	PRKD1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:31563800-31650000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:31564800-31648600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr14:31565600-31648000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr14:31566000-31627400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr14:31566200-31627000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr14:31566200-31635200	Strong transcription	Placenta	Placenta
7	chr14:31566200-31648200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr14:31567000-31620200	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr14:31567000-31647600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr14:31567000-31651200	Strong transcription	Dnd41	blood
11	chr14:31573000-31650200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:31573800-31648200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:31576800-31623800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:31588000-31623800	Weak transcription	Psoas Muscle	Psoas
15	chr14:31591800-31656400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:31593800-31648200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr14:31594400-31628600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr14:31594600-31619800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:31595000-31649000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr14:31595200-31630200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr14:31597600-31648400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr14:31598000-31648200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr14:31598200-31633200	Strong transcription	HepG2	liver
24	chr14:31598200-31648000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr14:31598200-31651200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr14:31598400-31627200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr14:31598400-31633200	Strong transcription	Liver	Liver
28	chr14:31598400-31648000	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr14:31598600-31620000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr14:31598600-31631000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr14:31598600-31632000	Weak transcription	Fetal Brain Male	brain
32	chr14:31598600-31633000	Weak transcription	Stomach Mucosa	stomach
33	chr14:31598600-31635400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr14:31598600-31648400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr14:31598600-31648400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr14:31598600-31648600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr14:31598600-31649000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr14:31598600-31649400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr14:31598800-31633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr14:31600600-31634400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr14:31600600-31649800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr14:31600800-31623600	Strong transcription	Osteobl	bone
43	chr14:31601200-31627200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr14:31601800-31619800	Strong transcription	HUVEC	blood vessel
45	chr14:31603800-31619400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr14:31603800-31621800	Strong transcription	Fetal Lung	lung
47	chr14:31603800-31653400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr14:31604400-31619400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr14:31605400-31633000	Strong transcription	Fetal Intestine Large	intestine
50	chr14:31605400-31635200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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