Variant report

Variant	rs9315725
Chromosome Location	chr13:40267806-40267807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40240996..40242613-chr13:40266490..40268729,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs3812882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4142370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4278626	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4312180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4384490	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408422	0.81[ASN][1000 genomes]
rs4415900	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943687	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943691	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563732	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67976778	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7325068	0.81[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7325655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7327779	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7332791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7334651	0.86[JPT][hapmap]
rs7335799	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7984958	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9315720	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9532408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9532410	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9532411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9532412	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9532413	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532414	1.00[CEU][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9548859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9548862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9548863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9548865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548870	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548893	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548894	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548896	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548901	0.81[CHB][hapmap]
rs9566471	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566472	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576874	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9576875	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9576881	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][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
rs9315725	COG6	cis	Muscle Skeletal	GTEx
rs9315725	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
2	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
5	chr13:40231600-40270200	Weak transcription	Gastric	stomach
6	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
8	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
9	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
10	chr13:40255000-40268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:40255000-40270000	Weak transcription	Lung	lung
12	chr13:40255000-40291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:40255200-40272800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:40255200-40291000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:40255400-40272800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:40255600-40270800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:40255600-40272800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr13:40255600-40283600	Weak transcription	Fetal Brain Male	brain
20	chr13:40255800-40271000	Weak transcription	Ovary	ovary
21	chr13:40255800-40283800	Weak transcription	Brain Anterior Caudate	brain
22	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
23	chr13:40257600-40274600	Weak transcription	HMEC	breast
24	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
25	chr13:40257800-40269200	Weak transcription	Fetal Kidney	kidney
26	chr13:40257800-40273200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr13:40258200-40289800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr13:40262000-40271200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr13:40262600-40294000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr13:40262800-40269000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr13:40262800-40270600	Weak transcription	Primary T cells from cord blood	blood
32	chr13:40262800-40270600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr13:40262800-40272800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:40262800-40272800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr13:40262800-40273600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:40262800-40279200	Weak transcription	HepG2	liver
37	chr13:40262800-40285600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr13:40262800-40286800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr13:40262800-40287200	Weak transcription	Fetal Muscle Leg	muscle
40	chr13:40262800-40291600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:40262800-40291600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:40262800-40291800	Weak transcription	Left Ventricle	heart
43	chr13:40262800-40293600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
45	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:40263000-40268800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr13:40263000-40272800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr13:40263000-40273600	Weak transcription	HSMM	muscle
49	chr13:40263000-40285600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr13:40263000-40288600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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