Variant report

Variant	rs4570710
Chromosome Location	chr13:40295129-40295130
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs4329796	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4346098	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7988187	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7989518	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9315726	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9548849	0.83[EUR][1000 genomes]
rs9548874	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548882	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9548886	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9548887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548889	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9548890	0.85[EUR][1000 genomes]
rs9548892	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9566464	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs9566468	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9576878	0.87[CEU][hapmap]
rs9576879	0.80[EUR][1000 genomes]
rs9576883	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9576885	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9576886	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9576888	0.80[AMR][1000 genomes];0.87[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4570710	COG6	cis	multi-tissue	Pritchard
rs4570710	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
2	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
3	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
5	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
6	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
7	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:40263000-40297200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr13:40263200-40302600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:40267000-40297400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:40267200-40296800	Weak transcription	Brain Hippocampus Middle	brain
12	chr13:40267200-40296800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr13:40267200-40297000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr13:40272000-40297400	Weak transcription	Ovary	ovary
16	chr13:40273800-40296200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:40274000-40301600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr13:40282400-40310800	Weak transcription	Right Ventricle	heart
20	chr13:40283600-40310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr13:40283600-40311000	Weak transcription	Gastric	stomach
22	chr13:40284000-40298200	Weak transcription	Brain Anterior Caudate	brain
23	chr13:40284200-40310400	Weak transcription	Fetal Stomach	stomach
24	chr13:40284400-40302200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
26	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
27	chr13:40287000-40303000	Weak transcription	NHLF	lung
28	chr13:40287200-40295200	Weak transcription	HepG2	liver
29	chr13:40287200-40297600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr13:40287400-40296600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr13:40287400-40311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr13:40287400-40311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:40287400-40313000	Weak transcription	NHEK	skin
34	chr13:40287600-40310800	Weak transcription	HSMMtube	muscle
35	chr13:40289200-40297400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr13:40289400-40297400	Weak transcription	Fetal Kidney	kidney
37	chr13:40290200-40311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr13:40290800-40296600	Weak transcription	Brain Substantia Nigra	brain
40	chr13:40290800-40299200	Strong transcription	Fetal Lung	lung
41	chr13:40291400-40298200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:40291400-40310800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr13:40291800-40297600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr13:40292000-40297200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr13:40292000-40298600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:40292000-40302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:40292000-40302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr13:40292000-40302800	Weak transcription	Fetal Intestine Small	intestine
49	chr13:40292000-40310400	Weak transcription	Fetal Brain Female	brain
50	chr13:40292000-40313400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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