Variant report

Variant	rs6503519
Chromosome Location	chr17:37706578-37706579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDK12-1	chr17:37706308-37707184	NONHSAT053446
2	lnc-CDK12-1	chr17:37706444-37706694	NONHSAT053450

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1054488	0.83[ASN][1000 genomes]
rs10775391	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1077715	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10852933	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078904	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11078905	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078906	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11078907	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11078910	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078911	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078912	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078913	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11078915	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654853	0.95[AFR][1000 genomes]
rs11654935	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11655531	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657058	0.85[ASN][1000 genomes]
rs11657153	0.85[ASN][1000 genomes]
rs11658219	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11658678	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11868029	0.81[ASN][1000 genomes]
rs11868030	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11870631	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12450559	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12452682	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12936646	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12936996	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12937013	0.81[ASN][1000 genomes]
rs12942352	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12942360	0.81[EUR][1000 genomes]
rs12942391	0.86[ASN][1000 genomes]
rs12947281	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12947506	0.86[ASN][1000 genomes]
rs12948906	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12952384	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1619021	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1874226	0.86[ASN][1000 genomes]
rs1877030	0.81[ASN][1000 genomes]
rs2018026	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2303316	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34957982	0.82[EUR][1000 genomes]
rs35335692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364989	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3889368	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs412430	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4239222	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4286140	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4332770	0.86[ASN][1000 genomes]
rs4357971	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4392104	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs439537	0.86[ASN][1000 genomes]
rs4462633	0.82[ASN][1000 genomes]
rs4488484	0.86[ASN][1000 genomes]
rs4794813	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794814	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795376	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4795377	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4795379	0.81[ASN][1000 genomes]
rs4795381	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795382	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4795384	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4795385	0.86[ASN][1000 genomes]
rs55660616	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62077464	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6503517	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6503518	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6503521	0.86[ASN][1000 genomes]
rs7216086	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219909	0.93[AFR][1000 genomes]
rs7225096	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7405770	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7406928	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7503069	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7503377	0.86[ASN][1000 genomes]
rs7503514	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7503705	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8065963	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8067884	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8069074	0.83[ASN][1000 genomes]
rs8075737	0.86[ASN][1000 genomes]
rs8081528	0.81[ASN][1000 genomes]
rs8081780	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8182252	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs903507	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
4	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers 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	44 gene(s)	inside rSNPs	diseases
6	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1063848	chr17:37575622-37707592	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
11	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6503519	PGAP3	cis	Heart Left Ventricle	GTEx
rs6503519	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37683800-37719400	Weak transcription	Psoas Muscle	Psoas
2	chr17:37687400-37706600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:37687800-37709600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr17:37687800-37729800	Weak transcription	Small Intestine	intestine
5	chr17:37688000-37707400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr17:37688400-37708000	Weak transcription	Gastric	stomach
7	chr17:37688400-37709600	Weak transcription	Colonic Mucosa	Colon
8	chr17:37688400-37711600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr17:37688400-37711600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:37689000-37707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:37689000-37708000	Weak transcription	NH-A	brain
12	chr17:37689000-37719400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr17:37689200-37711600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:37690800-37709400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr17:37693000-37719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr17:37695400-37727400	Weak transcription	K562	blood
17	chr17:37695600-37707200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:37695800-37707200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:37695800-37707400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr17:37695800-37707800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:37695800-37712400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr17:37695800-37723200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr17:37697400-37709600	Weak transcription	HMEC	breast
24	chr17:37699200-37706600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:37699800-37706800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr17:37699800-37714800	Strong transcription	Ovary	ovary
27	chr17:37700000-37708000	Weak transcription	Pancreas	Pancrea
28	chr17:37700200-37725800	Strong transcription	Placenta	Placenta
29	chr17:37700400-37709600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:37701000-37707000	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr17:37701000-37714600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr17:37701000-37714800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:37701000-37714800	Strong transcription	Brain Anterior Caudate	brain
34	chr17:37701000-37719400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:37701000-37728800	Strong transcription	Liver	Liver
36	chr17:37701200-37707400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:37701200-37707600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:37701200-37708200	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr17:37701200-37710600	Strong transcription	Brain Hippocampus Middle	brain
40	chr17:37701200-37727600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr17:37701400-37708200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr17:37702400-37708600	Strong transcription	Brain Substantia Nigra	brain
43	chr17:37702400-37717600	Strong transcription	Thymus	Thymus
44	chr17:37702600-37709400	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr17:37702600-37710800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:37702600-37715000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr17:37702800-37706600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr17:37702800-37706800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr17:37702800-37706800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr17:37702800-37710800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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