Variant report

Variant	rs9349005
Chromosome Location	chr6:36640368-36640369
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1010423	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1010424	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10456441	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10456442	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10456443	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1059234	0.85[JPT][hapmap]
rs10807170	0.80[LWK][hapmap]
rs10947616	0.84[ASN][1000 genomes]
rs10947618	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10947619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947620	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947622	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10947623	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758192	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12174270	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192827	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12192877	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12203953	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12206430	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12210094	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12214686	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12524435	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12528248	0.90[JPT][hapmap]
rs12528913	0.85[ASN][1000 genomes]
rs12530170	1.00[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1801270	0.90[JPT][hapmap]
rs3829963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829965	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4464789	0.87[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4711458	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711459	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711460	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711461	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4711462	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713993	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4714002	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4714003	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58714705	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6457932	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6457934	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457935	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6915170	0.80[ASN][1000 genomes]
rs6920453	0.84[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6931097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72853320	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7382183	0.85[ASN][1000 genomes]
rs7747146	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7757749	0.90[JPT][hapmap]
rs7761648	0.90[JPT][hapmap]
rs876581	0.90[JPT][hapmap]
rs9349002	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349003	0.84[ASN][1000 genomes]
rs9357222	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9366912	0.87[ASW][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9394371	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031191	chr6:36588974-36718015	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv538201	chr6:36588974-36718015	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv602946	chr6:36633160-36641478	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
4	nsv602947	chr6:36637597-36641157	Enhancers Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	esv13626	chr6:36640176-36642182	Enhancers Weak transcription	CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9349005	MAPK13	cis	parietal	SCAN
rs9349005	MLN	cis	cerebellum	SCAN
rs9349005	CDKN1A	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36631000-36644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:36635200-36643800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:36635400-36644000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:36635400-36645600	Weak transcription	Small Intestine	intestine
5	chr6:36635600-36644000	Weak transcription	Hela-S3	cervix
6	chr6:36636000-36640800	Enhancers	Fetal Intestine Small	intestine
7	chr6:36636400-36643800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:36636400-36643800	Weak transcription	NH-A	brain
9	chr6:36636800-36641000	Enhancers	Fetal Intestine Large	intestine
10	chr6:36637000-36643800	Weak transcription	Osteobl	bone
11	chr6:36637200-36641600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:36637200-36641600	Weak transcription	GM12878-XiMat	blood
13	chr6:36637200-36643600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:36637200-36643800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:36637200-36643800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:36637200-36643800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:36637200-36643800	Weak transcription	HSMM	muscle
18	chr6:36637400-36642600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:36637800-36642600	Weak transcription	HSMMtube	muscle
20	chr6:36637800-36643400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:36637800-36643400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:36637800-36643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:36637800-36643800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:36638800-36644200	Weak transcription	Ovary	ovary
25	chr6:36639600-36640400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr6:36640000-36643800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:36640000-36643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:36640000-36644000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:36640200-36641600	Weak transcription	Placenta	Placenta
30	chr6:36640200-36642000	Weak transcription	HepG2	liver
31	chr6:36640200-36642400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:36640200-36643800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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