Variant report

Variant	rs9943
Chromosome Location	chr13:40326282-40326283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11618582	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12872801	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12875311	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12876235	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28635831	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34394770	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4514547	0.87[GIH][hapmap];0.85[TSI][hapmap]
rs4569133	0.87[GIH][hapmap];0.85[TSI][hapmap]
rs4598779	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7319041	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7320598	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7330016	0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7986796	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7989997	0.87[AFR][1000 genomes]
rs7991151	0.87[GIH][hapmap];0.85[TSI][hapmap]
rs7993214	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8002731	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9532430	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9532433	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9532434	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9548932	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9594366	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9603603	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9603605	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9603608	0.92[CEU][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9603610	0.87[AFR][1000 genomes]
rs9603611	0.87[AFR][1000 genomes]
rs9603612	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9603616	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9943	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
2	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
5	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
9	chr13:40294600-40327800	Weak transcription	NH-A	brain
10	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
11	chr13:40297800-40329800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr13:40299200-40327600	Weak transcription	Fetal Heart	heart
13	chr13:40302000-40328800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:40304000-40328800	Weak transcription	Dnd41	blood
15	chr13:40304600-40340000	Weak transcription	Osteobl	bone
16	chr13:40306400-40327400	Weak transcription	HUVEC	blood vessel
17	chr13:40307600-40329400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr13:40309200-40331400	Weak transcription	Stomach Mucosa	stomach
19	chr13:40309200-40334600	Weak transcription	HepG2	liver
20	chr13:40311400-40347200	Weak transcription	HSMM	muscle
21	chr13:40311600-40326600	Weak transcription	Placenta	Placenta
22	chr13:40311600-40329400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr13:40311600-40331200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr13:40311600-40339800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr13:40311600-40340000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr13:40311800-40331000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:40311800-40339800	Weak transcription	Brain Anterior Caudate	brain
28	chr13:40311800-40340000	Weak transcription	Ovary	ovary
29	chr13:40312000-40340000	Weak transcription	Brain Angular Gyrus	brain
30	chr13:40312200-40327000	Weak transcription	Primary T cells from cord blood	blood
31	chr13:40312200-40327000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr13:40312200-40327400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:40312200-40329000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr13:40312200-40329800	Weak transcription	Aorta	Aorta
35	chr13:40312200-40331800	Weak transcription	Left Ventricle	heart
36	chr13:40312200-40333000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr13:40312200-40340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:40312200-40340000	Weak transcription	Pancreas	Pancrea
39	chr13:40312200-40340200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:40312400-40329400	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr13:40312400-40329400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr13:40312400-40329800	Weak transcription	Fetal Stomach	stomach
44	chr13:40314600-40331400	Weak transcription	Primary B cells from cord blood	blood
45	chr13:40315000-40340200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr13:40315200-40330600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr13:40315400-40329000	Weak transcription	Fetal Kidney	kidney
48	chr13:40320600-40329400	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:40322000-40326400	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:40323000-40329400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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