Variant report

Variant	rs2765341
Chromosome Location	chr13:111270363-111270364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111270127..111273388-chr13:111363315..111367711,4	MCF-7	breast:
2	chr13:111268040..111269954-chr13:111270156..111273298,3	K562	blood:
3	chr13:111270148..111271814-chr13:111272109..111273731,2	K562	blood:
4	chr13:111266965..111271727-chr13:111364973..111369025,9	MCF-7	breast:
5	chr13:111265756..111270693-chr13:111363417..111370660,10	K562	blood:

Variant related genes	Relation type
ENSG00000153487	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1043886	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11551105	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16940507	0.95[EUR][1000 genomes]
rs179356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs191322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2986320	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330543	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330546	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330549	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs330557	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs330559	0.95[EUR][1000 genomes]
rs330569	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs330570	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap]
rs330572	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs371162	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3759463	1.00[CEU][hapmap];0.84[TSI][hapmap];0.95[EUR][1000 genomes]
rs379324	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs380564	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs389541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41275126	0.94[EUR][1000 genomes]
rs41275128	0.97[EUR][1000 genomes]
rs412822	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs422789	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs440771	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs441805	0.87[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs61969236	0.85[EUR][1000 genomes]
rs61970483	0.95[EUR][1000 genomes]
rs61970484	0.95[EUR][1000 genomes]
rs61970486	0.94[EUR][1000 genomes]
rs61970489	0.95[EUR][1000 genomes]
rs61970494	0.90[EUR][1000 genomes]
rs61970495	0.81[EUR][1000 genomes]
rs9559854	0.85[EUR][1000 genomes]

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	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	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
13	nsv1038089	chr13:111229517-111274823	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
14	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
15	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
16	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	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
18	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2765341	CARS2	cis	Lymphoblastoid	GTEx
rs2765341	CARKD	cis	Whole Blood	GTEx
rs2765341	CARKD	cis	parietal	SCAN
rs2765341	CARS2	cis	parietal	SCAN
rs2765341	SLC17A6	trans	cerebellum	SCAN
rs2765341	LIG4	cis	cerebellum	SCAN
rs2765341	CARS2	cis	lymphoblastoid	seeQTL
rs2765341	AL139385.1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111268400-111270400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr13:111268600-111270400	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr13:111268800-111270400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr13:111268800-111270400	Flanking Active TSS	HMEC	breast
5	chr13:111269000-111270400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr13:111269000-111270400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:111269000-111270400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:111269000-111270400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:111269000-111270400	Flanking Active TSS	Liver	Liver
10	chr13:111269000-111270400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr13:111269000-111270400	Enhancers	Placenta	Placenta
12	chr13:111269000-111270400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr13:111269000-111272200	Enhancers	Pancreas	Pancrea
14	chr13:111269000-111277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr13:111269000-111277600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr13:111269200-111270400	Enhancers	Brain Substantia Nigra	brain
18	chr13:111269200-111270400	Enhancers	Fetal Heart	heart
19	chr13:111269200-111270400	Enhancers	Fetal Muscle Leg	muscle
20	chr13:111269200-111270400	Enhancers	Fetal Thymus	thymus
21	chr13:111269200-111270400	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr13:111269200-111270400	Flanking Active TSS	GM12878-XiMat	blood
23	chr13:111269200-111270600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr13:111269200-111271000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr13:111269200-111271000	Enhancers	Fetal Stomach	stomach
26	chr13:111269200-111271400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:111269200-111271400	Enhancers	Stomach Mucosa	stomach
28	chr13:111269200-111274600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr13:111269400-111270400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr13:111269400-111270400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr13:111269400-111270400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:111269400-111270400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr13:111269400-111270400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr13:111269400-111270400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr13:111269400-111270400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:111269400-111270400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr13:111269400-111270400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:111269400-111270400	Enhancers	Adipose Nuclei	Adipose
39	chr13:111269400-111270400	Enhancers	Brain Angular Gyrus	brain
40	chr13:111269400-111270400	Enhancers	Brain Germinal Matrix	brain
41	chr13:111269400-111270400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr13:111269400-111270400	Enhancers	Colonic Mucosa	Colon
43	chr13:111269400-111270400	Enhancers	Fetal Kidney	kidney
44	chr13:111269400-111270400	Flanking Active TSS	HepG2	liver
45	chr13:111269400-111270400	Enhancers	HSMM	muscle
46	chr13:111269400-111270600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr13:111269400-111270800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:111269400-111270800	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr13:111269400-111270800	Enhancers	NHDF-Ad	bronchial
50	chr13:111269400-111271200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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