Variant report

Variant	rs3759463
Chromosome Location	chr13:111286592-111286593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:111286529-111288451	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:111286262..111288544-chr13:111335123..111337975,2	K562	blood:
2	chr13:111286170..111289373-chr13:111362877..111366767,3	K562	blood:
3	chr13:111285638..111287730-chr13:111364678..111367940,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255831	TF binding region
ENSG00000134905	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1043886	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11551105	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16940507	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs179356	1.00[CEU][hapmap];0.84[TSI][hapmap];0.95[EUR][1000 genomes]
rs191322	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2765341	1.00[CEU][hapmap];0.84[TSI][hapmap];0.95[EUR][1000 genomes]
rs2986320	0.91[EUR][1000 genomes]
rs330542	0.95[EUR][1000 genomes]
rs330543	0.95[EUR][1000 genomes]
rs330544	0.95[EUR][1000 genomes]
rs330545	0.95[EUR][1000 genomes]
rs330546	0.95[EUR][1000 genomes]
rs330547	0.95[EUR][1000 genomes]
rs330548	0.95[EUR][1000 genomes]
rs330549	0.94[EUR][1000 genomes]
rs330551	0.89[EUR][1000 genomes]
rs330557	0.93[EUR][1000 genomes]
rs330559	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs330569	0.87[EUR][1000 genomes]
rs330570	0.82[CEU][hapmap]
rs330572	0.95[EUR][1000 genomes]
rs371162	0.95[EUR][1000 genomes]
rs379324	0.95[EUR][1000 genomes]
rs380564	0.92[EUR][1000 genomes]
rs389541	1.00[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.99[EUR][1000 genomes]
rs41275126	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41275128	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs412822	0.95[EUR][1000 genomes]
rs422789	0.92[EUR][1000 genomes]
rs440771	0.95[EUR][1000 genomes]
rs61969236	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61970483	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61970484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61970486	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61970489	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61970494	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61970495	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9559854	0.90[EUR][1000 genomes]
rs9588217	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic 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 miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
13	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription 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	240 gene(s)	inside rSNPs	diseases
16	nsv456120	chr13:111280002-111309617	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
17	nsv563125	chr13:111280002-111309617	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
18	nsv1042232	chr13:111282123-111348475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3759463	CARKD	cis	parietal	SCAN
rs3759463	CARKD	cis	Whole Blood	GTEx
rs3759463	FLJ10769	cis	multi-tissue	Pritchard
rs3759463	CARS2	cis	parietal	SCAN
rs3759463	FLJ12118	cis	multi-tissue	Pritchard
rs3759463	SLC17A6	trans	cerebellum	SCAN
rs3759463	LIG4	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:111269400-111286600	Weak transcription	Fetal Brain Male	brain
3	chr13:111269400-111287200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr13:111270800-111296800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:111271200-111287000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr13:111275600-111287400	Weak transcription	K562	blood
7	chr13:111277800-111286800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr13:111278000-111286600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:111278000-111286600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:111278200-111286800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr13:111278400-111287200	Weak transcription	Small Intestine	intestine
12	chr13:111278600-111286800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:111279600-111286800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr13:111279600-111286800	Weak transcription	Stomach Mucosa	stomach
15	chr13:111280400-111287000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr13:111280800-111286600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:111280800-111286600	Weak transcription	Brain Angular Gyrus	brain
18	chr13:111280800-111328600	Weak transcription	Psoas Muscle	Psoas
19	chr13:111281200-111286800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:111281400-111286600	Weak transcription	Brain Germinal Matrix	brain
21	chr13:111281400-111286800	Weak transcription	Left Ventricle	heart
22	chr13:111281400-111287200	Weak transcription	Fetal Heart	heart
23	chr13:111281400-111288600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:111281400-111293000	Weak transcription	Right Atrium	heart
25	chr13:111281600-111286600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr13:111281600-111286600	Weak transcription	Right Ventricle	heart
27	chr13:111281600-111286800	Weak transcription	Brain Substantia Nigra	brain
28	chr13:111281600-111287000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr13:111281600-111287000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:111281600-111287000	Weak transcription	HMEC	breast
31	chr13:111282000-111286800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr13:111282000-111309600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:111282400-111286600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr13:111282400-111286600	Weak transcription	NHLF	lung
35	chr13:111282400-111286800	Weak transcription	Colonic Mucosa	Colon
36	chr13:111282400-111286800	Weak transcription	Fetal Lung	lung
37	chr13:111282800-111310000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr13:111283200-111286600	Weak transcription	Brain Anterior Caudate	brain
39	chr13:111283400-111286600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr13:111283400-111286800	Weak transcription	Esophagus	oesophagus
41	chr13:111283400-111286800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr13:111283600-111286600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:111283600-111286600	Weak transcription	Aorta	Aorta
44	chr13:111283600-111286600	Weak transcription	Pancreas	Pancrea
45	chr13:111283600-111286600	Weak transcription	Spleen	Spleen
46	chr13:111283600-111286600	Weak transcription	HSMMtube	muscle
47	chr13:111283800-111286600	Weak transcription	Ovary	ovary
48	chr13:111283800-111286600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr13:111283800-111286800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr13:111283800-111286800	Weak transcription	Primary B cells from cord blood	blood

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