Variant report

Variant	rs36563
Chromosome Location	chr14:71352648-71352649
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17108910	0.89[TSI][hapmap]
rs1859915	0.89[TSI][hapmap]
rs2051864	0.89[TSI][hapmap]
rs2526866	0.82[EUR][1000 genomes]
rs36562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1049741	chr14:71233043-71462509	Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1039769	chr14:71310954-71525720	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv542128	chr14:71310954-71525720	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1053303	chr14:71316325-71402971	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alcohol dependence	19581569	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs36563	KCTD13	trans	cerebellum	SCAN
rs36563	PCNX	cis	cerebellum	SCAN
rs36563	PCNX	cis	parietal	SCAN
rs36563	CARD6	trans	parietal	SCAN
rs36563	PCNX	Cis_1M	lymphoblastoid	RTeQTL
rs36563	ZFYVE1	cis	cerebellum	SCAN
rs36563	PCNX	cis	Nerve Tibial	GTEx
rs36563	PCNX	cis	Artery Tibial	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71339600-71354600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:71348200-71352800	Enhancers	Primary hematopoietic stem cells	blood
3	chr14:71348600-71352800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:71348600-71353000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr14:71348800-71354600	Weak transcription	Small Intestine	intestine
6	chr14:71349000-71353400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr14:71349200-71353200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr14:71349400-71352800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:71349400-71353200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr14:71349600-71352800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr14:71349600-71353200	Enhancers	Primary T cells fromperipheralblood	blood
12	chr14:71349600-71353200	Enhancers	Duodenum Mucosa	Duodenum
13	chr14:71349600-71353400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr14:71349800-71356000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr14:71349800-71356200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr14:71350000-71353200	Weak transcription	Thymus	Thymus
17	chr14:71350000-71356200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr14:71350200-71353400	Weak transcription	Hela-S3	cervix
19	chr14:71350200-71354200	Weak transcription	HSMMtube	muscle
20	chr14:71350400-71353400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr14:71350400-71353800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:71350400-71353800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr14:71350400-71353800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr14:71350400-71354400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr14:71350400-71354400	Weak transcription	HSMM	muscle
26	chr14:71350600-71352800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr14:71350600-71353400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr14:71350600-71353400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:71350600-71353400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:71350600-71353400	Weak transcription	Osteobl	bone
31	chr14:71350600-71353600	Weak transcription	NHLF	lung
32	chr14:71350600-71353800	Weak transcription	NHDF-Ad	bronchial
33	chr14:71350600-71354000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr14:71350600-71354200	Weak transcription	Adipose Nuclei	Adipose
35	chr14:71350600-71355600	Enhancers	Primary B cells from cord blood	blood
36	chr14:71350600-71356600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr14:71350600-71373000	Weak transcription	Spleen	Spleen
38	chr14:71350800-71353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr14:71351000-71355000	Flanking Active TSS	GM12878-XiMat	blood
40	chr14:71351200-71353000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr14:71351200-71353000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr14:71351200-71357400	Enhancers	Fetal Thymus	thymus
43	chr14:71351800-71353000	Weak transcription	K562	blood
44	chr14:71351800-71353400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr14:71351800-71353400	Weak transcription	NH-A	brain
46	chr14:71351800-71356000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:71351800-71361000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:71351800-71365200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr14:71352000-71353600	Weak transcription	HMEC	breast
50	chr14:71352000-71353800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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