Variant report

Variant	rs9366617
Chromosome Location	chr6:25327270-25327271
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	chr6:25318943..25320704-chr6:25326151..25329125,2	K562	blood:
2	chr6:25326407..25328243-chr6:25331824..25333958,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs16890366	0.83[AFR][1000 genomes]
rs2143023	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2690107	0.94[MEX][hapmap];0.87[TSI][hapmap]
rs2690111	0.89[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs4712904	0.82[LWK][hapmap]
rs4712905	0.84[LWK][hapmap]
rs4712906	0.82[AFR][1000 genomes]
rs4712907	0.82[AFR][1000 genomes]
rs55967593	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58191968	0.82[AFR][1000 genomes]
rs60084615	0.82[AFR][1000 genomes]
rs6456664	0.82[AFR][1000 genomes]
rs6456665	0.82[AFR][1000 genomes]
rs6903148	0.82[AFR][1000 genomes]
rs6906812	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6908260	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6913606	0.83[AFR][1000 genomes]
rs6913886	0.83[AFR][1000 genomes]
rs6914439	0.82[AFR][1000 genomes]
rs6914514	0.82[AFR][1000 genomes]
rs6914654	0.82[AFR][1000 genomes]
rs6914798	0.82[AFR][1000 genomes]
rs6914930	0.82[AFR][1000 genomes]
rs6915270	0.81[AFR][1000 genomes]
rs6917631	0.82[AFR][1000 genomes]
rs6921343	0.82[AFR][1000 genomes]
rs6927238	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6932783	0.83[ASN][1000 genomes]
rs6938281	0.82[AFR][1000 genomes]
rs7741580	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7743750	0.83[AFR][1000 genomes]
rs7746942	0.81[ASW][hapmap];0.93[LWK][hapmap]
rs7746969	0.82[AFR][1000 genomes]
rs7755701	0.83[AFR][1000 genomes]
rs7756143	0.83[AFR][1000 genomes]
rs7758529	0.80[AFR][1000 genomes]
rs7759796	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7759828	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7759879	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7760067	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760151	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7764111	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9295654	0.81[ASW][hapmap];0.93[LWK][hapmap];0.83[AFR][1000 genomes]
rs9295655	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348671	0.83[AFR][1000 genomes]
rs9348672	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9356974	0.82[AFR][1000 genomes]
rs9366615	0.84[JPT][hapmap]
rs9366616	0.82[AFR][1000 genomes]
rs9366618	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9379752	0.82[AFR][1000 genomes]
rs9379753	0.82[AFR][1000 genomes]
rs9393639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9393640	0.94[ASN][1000 genomes]
rs9461132	0.82[AFR][1000 genomes]
rs9461134	0.80[AFR][1000 genomes]
rs9461135	0.82[AFR][1000 genomes]
rs9461136	0.82[AFR][1000 genomes]
rs9467466	0.81[ASW][hapmap];0.93[LWK][hapmap];0.82[AFR][1000 genomes]
rs999039	0.87[ASW][hapmap];0.93[LWK][hapmap];0.81[TSI][hapmap];0.85[AFR][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	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883487	chr6:25280119-25508868	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9366617	LRRC16A	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25306600-25331400	Weak transcription	Spleen	Spleen
2	chr6:25313400-25329800	Weak transcription	Primary T cells from cord blood	blood
3	chr6:25313800-25331400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:25315400-25329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:25321000-25329400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:25321000-25329600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:25321000-25331400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:25321200-25329200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:25321200-25329400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:25321200-25329400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:25321600-25329200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:25321600-25329400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr6:25321600-25329600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:25321600-25329800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:25321600-25341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr6:25323000-25333200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:25324600-25328000	Weak transcription	Brain Germinal Matrix	brain
18	chr6:25324600-25329200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:25324600-25329600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:25324600-25330400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:25324600-25331600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:25325000-25327400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:25325000-25329400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:25325000-25331600	Weak transcription	Adipose Nuclei	Adipose
25	chr6:25325200-25327400	Weak transcription	Fetal Intestine Small	intestine
26	chr6:25325200-25327600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr6:25325200-25328800	Enhancers	Fetal Heart	heart
28	chr6:25325200-25329400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:25325200-25330200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:25325200-25330200	Weak transcription	Esophagus	oesophagus
31	chr6:25325200-25331400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:25325200-25331400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:25325200-25331400	Weak transcription	Placenta	Placenta
34	chr6:25325200-25331400	Weak transcription	Pancreas	Pancrea
35	chr6:25325200-25331400	Weak transcription	HSMMtube	muscle
36	chr6:25325200-25336400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:25325200-25336400	Weak transcription	Lung	lung
38	chr6:25326200-25328000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:25326600-25327600	Enhancers	Small Intestine	intestine
40	chr6:25326600-25327800	Enhancers	Aorta	Aorta
41	chr6:25326600-25328600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr6:25326600-25329200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:25326800-25327600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr6:25326800-25327600	Enhancers	Brain Anterior Caudate	brain
45	chr6:25326800-25327600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr6:25326800-25333000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr6:25327000-25328600	Enhancers	Duodenum Mucosa	Duodenum
48	chr6:25327000-25329200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:25327000-25332600	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:25327200-25327400	Enhancers	Pancreatic Islets	Pancreatic Islet

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