Variant report

Variant	rs9349687
Chromosome Location	chr6:53760749-53760750
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs55906536	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9349688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357772	0.81[CHB][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs9370243	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9395885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9349687	MKNK2	trans	brain	seeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
3	chr6:53739000-53767800	Weak transcription	Ovary	ovary
4	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
5	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
8	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
9	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
11	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
12	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:53746400-53762000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:53746800-53762000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
17	chr6:53749000-53761800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:53749200-53763600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:53749200-53765800	Weak transcription	Primary T cells from cord blood	blood
20	chr6:53749400-53762600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:53752400-53761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:53752400-53771000	Weak transcription	Gastric	stomach
23	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:53754400-53760800	Weak transcription	NH-A	brain
26	chr6:53754800-53761000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:53754800-53779800	Weak transcription	NHLF	lung
29	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:53756000-53760800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:53756000-53761000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:53756200-53761200	Weak transcription	HUVEC	blood vessel
34	chr6:53756200-53762000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:53757800-53767400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:53757800-53768000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:53758800-53761400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:53759200-53760800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:53759200-53762400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:53759200-53762400	Weak transcription	Left Ventricle	heart
42	chr6:53759200-53767600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr6:53759200-53767600	Weak transcription	Lung	lung
44	chr6:53759200-53767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:53759200-53769400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr6:53759200-53770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
48	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
49	chr6:53759400-53760800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr6:53759400-53761000	Weak transcription	Placenta Amnion	Placenta Amnion

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