Variant report

Variant	rs9315729
Chromosome Location	chr13:40345191-40345192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40338587..40340138-chr13:40344634..40347298,2	MCF-7	breast:
2	chr13:40343415..40346498-chr13:40346695..40349589,3	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11147769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618960	0.86[AFR][1000 genomes]
rs17591231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591266	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3812882	0.81[JPT][hapmap]
rs3812883	0.82[JPT][hapmap]
rs3812884	0.82[JPT][hapmap]
rs3812885	0.82[JPT][hapmap]
rs3812886	0.82[JPT][hapmap]
rs3812887	0.82[JPT][hapmap]
rs3812888	0.81[JPT][hapmap]
rs4133063	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs4142370	0.82[JPT][hapmap]
rs4245396	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4288869	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs4338665	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403927	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408422	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4409964	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941936	0.90[JPT][hapmap]
rs4941937	0.82[JPT][hapmap]
rs4941938	0.82[JPT][hapmap]
rs4943686	0.82[JPT][hapmap]
rs4943694	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943695	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943696	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7319128	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325068	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7325655	0.82[JPT][hapmap]
rs7327779	0.81[JPT][hapmap]
rs7327824	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330211	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs7334651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7337585	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984113	0.81[JPT][hapmap]
rs7998641	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8000009	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs9315720	0.82[JPT][hapmap]
rs9315730	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532408	0.82[JPT][hapmap]
rs9532412	0.81[JPT][hapmap]
rs9532429	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532432	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9532436	0.91[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9532439	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9548857	0.82[JPT][hapmap]
rs9548859	0.82[JPT][hapmap]
rs9548862	0.82[JPT][hapmap]
rs9548863	0.81[JPT][hapmap]
rs9548865	0.81[JPT][hapmap]
rs9548866	0.81[JPT][hapmap]
rs9548867	0.82[JPT][hapmap]
rs9548868	0.81[JPT][hapmap]
rs9548869	0.81[JPT][hapmap]
rs9548898	0.83[AFR][1000 genomes]
rs9548900	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9548901	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548906	0.89[YRI][hapmap]
rs9548913	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs9548916	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548918	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548919	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548920	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548922	0.86[AFR][1000 genomes]
rs9548926	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548927	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9548928	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548929	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566474	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576881	0.81[JPT][hapmap]
rs9576882	0.81[JPT][hapmap]
rs9576891	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576892	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576894	0.81[YRI][hapmap];0.83[AFR][1000 genomes]
rs9576895	0.84[AFR][1000 genomes]
rs9576896	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576897	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576898	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs9315729	COG6	cis	Muscle Skeletal	GTEx
rs9315729	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40311400-40347200	Weak transcription	HSMM	muscle
2	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40327400-40352200	Weak transcription	Primary T cells from cord blood	blood
4	chr13:40327800-40347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:40330000-40345200	Weak transcription	Aorta	Aorta
6	chr13:40340400-40347000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:40340400-40347800	Weak transcription	HUVEC	blood vessel
8	chr13:40340400-40353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
10	chr13:40340600-40345800	Weak transcription	Left Ventricle	heart
11	chr13:40340600-40351200	Weak transcription	Gastric	stomach
12	chr13:40340600-40351200	Weak transcription	Right Ventricle	heart
13	chr13:40341000-40346800	Weak transcription	Fetal Stomach	stomach
14	chr13:40341400-40350600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr13:40342200-40348000	Weak transcription	Ovary	ovary
17	chr13:40342400-40350200	Weak transcription	HSMMtube	muscle
18	chr13:40342600-40347800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:40342600-40351200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:40342600-40360200	Weak transcription	Fetal Muscle Leg	muscle
21	chr13:40342800-40351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr13:40343600-40349200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr13:40344000-40345600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr13:40344200-40345400	Enhancers	Liver	Liver
25	chr13:40344400-40345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:40344400-40345200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr13:40344400-40345200	Enhancers	Adipose Nuclei	Adipose
28	chr13:40344800-40345200	Weak transcription	Brain Anterior Caudate	brain

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