Variant report

Variant	rs4409964
Chromosome Location	chr13:40342741-40342742
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11147769	0.99[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17591266	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3812882	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs3812883	0.81[JPT][hapmap]
rs3812884	0.81[JPT][hapmap]
rs3812885	0.81[JPT][hapmap]
rs3812886	0.81[JPT][hapmap]
rs3812887	0.81[JPT][hapmap]
rs3812888	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs4133063	0.94[ASW][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs4142370	0.81[JPT][hapmap]
rs4245396	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4288869	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs4338665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403927	1.00[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]
rs4941936	0.90[JPT][hapmap]
rs4941937	0.81[JPT][hapmap]
rs4941938	0.81[JPT][hapmap]
rs4941939	0.86[CHD][hapmap];0.85[GIH][hapmap];0.84[TSI][hapmap]
rs4943686	0.81[JPT][hapmap]
rs4943694	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4943695	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943696	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7319128	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325068	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][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	0.81[JPT][hapmap]
rs7327779	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs7327824	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330211	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs7334651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[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	0.84[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs7998641	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8000009	0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs9315720	0.81[JPT][hapmap]
rs9315729	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315730	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532408	0.81[JPT][hapmap]
rs9532412	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs9532420	0.86[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs9532429	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532432	0.89[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[CHD][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9532439	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9548857	0.81[JPT][hapmap]
rs9548859	0.81[JPT][hapmap]
rs9548862	0.81[JPT][hapmap]
rs9548863	0.81[JPT][hapmap]
rs9548865	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs9548866	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs9548867	0.81[JPT][hapmap]
rs9548868	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs9548869	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs9548880	0.84[CHD][hapmap];0.85[GIH][hapmap];0.86[TSI][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];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548906	0.88[ASW][hapmap];0.89[YRI][hapmap]
rs9548913	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs9548916	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[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];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548918	0.91[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	0.91[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	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548927	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9548928	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548929	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548930	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566474	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576881	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs9576882	0.84[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs9576891	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576892	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576894	0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs9576895	0.85[AFR][1000 genomes]
rs9576896	0.99[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	0.99[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
rs4409964	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs4409964	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

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	chr13:40327400-40344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:40327400-40352200	Weak transcription	Primary T cells from cord blood	blood
5	chr13:40327800-40347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:40330000-40345200	Weak transcription	Aorta	Aorta
7	chr13:40339200-40342800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr13:40339400-40342800	Enhancers	Fetal Brain Female	brain
9	chr13:40339600-40343200	Enhancers	Brain Germinal Matrix	brain
10	chr13:40339800-40343200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr13:40340000-40343000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:40340400-40347000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:40340400-40347800	Weak transcription	HUVEC	blood vessel
14	chr13:40340400-40353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
16	chr13:40340600-40345800	Weak transcription	Left Ventricle	heart
17	chr13:40340600-40351200	Weak transcription	Gastric	stomach
18	chr13:40340600-40351200	Weak transcription	Right Ventricle	heart
19	chr13:40341000-40344200	Weak transcription	Liver	Liver
20	chr13:40341000-40346800	Weak transcription	Fetal Stomach	stomach
21	chr13:40341200-40342800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr13:40341200-40343000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:40341200-40343200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr13:40341400-40350600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:40341800-40342800	Enhancers	Primary B cells from peripheral blood	blood
26	chr13:40341800-40342800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr13:40341800-40342800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr13:40341800-40342800	Enhancers	Esophagus	oesophagus
29	chr13:40341800-40342800	Enhancers	Psoas Muscle	Psoas
30	chr13:40341800-40343000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:40342000-40342800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr13:40342200-40343400	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr13:40342200-40343400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr13:40342200-40348000	Weak transcription	Ovary	ovary
36	chr13:40342400-40342800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr13:40342400-40342800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:40342400-40342800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr13:40342400-40342800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr13:40342400-40342800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr13:40342400-40342800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr13:40342400-40342800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr13:40342400-40342800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr13:40342400-40343400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr13:40342400-40350200	Weak transcription	HSMMtube	muscle
46	chr13:40342600-40343000	Weak transcription	Lung	lung
47	chr13:40342600-40344000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:40342600-40344200	Weak transcription	Brain Anterior Caudate	brain
49	chr13:40342600-40344400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr13:40342600-40344400	Weak transcription	Adipose Nuclei	Adipose

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