Variant report

Variant	rs40311
Chromosome Location	chr16:11963190-11963191
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:11950150..11954789-chr16:11962017..11966243,4	MCF-7	breast:
2	chr16:11944120..11947229-chr16:11960940..11964317,3	MCF-7	breast:
3	chr16:11943823..11946551-chr16:11960256..11963232,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263307	Chromatin interaction
ENSG00000171490	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10852344	0.80[MEX][hapmap]
rs11075022	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11075030	0.84[CHD][hapmap];0.80[MEX][hapmap]
rs11075032	0.80[MEX][hapmap]
rs11570136	0.80[CEU][hapmap]
rs11646545	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11647818	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11649405	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12925740	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs153025	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs154148	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171656	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2018199	0.88[CEU][hapmap]
rs2075158	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs2075159	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs251723	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28279	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs33619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33620	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33635	0.88[CEU][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs33637	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs33639	0.88[CHD][hapmap];0.80[MEX][hapmap]
rs33640	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33643	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33645	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33647	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33648	0.83[EUR][1000 genomes]
rs33649	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs33651	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33652	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33653	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33654	0.85[EUR][1000 genomes]
rs33655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs33659	0.85[ASW][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs33660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35153773	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3850997	0.80[TSI][hapmap]
rs42424	0.81[EUR][1000 genomes]
rs4493057	0.80[CEU][hapmap]
rs4511557	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs456325	0.88[CEU][hapmap]
rs718081	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes]
rs7185589	0.87[ASN][1000 genomes]
rs7193470	0.81[ASN][1000 genomes]
rs7197111	0.82[AMR][1000 genomes]
rs7198817	0.92[CEU][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7202234	0.92[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8046617	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8047726	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8059891	0.84[CEU][hapmap]
rs8061189	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs40311	TNFRSF17	cis	parietal	SCAN
rs40311	TNFRSF17	cis	cerebellum	SCAN
rs40311	RSL1D1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11946200-11975600	Weak transcription	Aorta	Aorta
2	chr16:11946400-11969400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:11946400-11969400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr16:11946400-11969400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:11946400-11975600	Weak transcription	Esophagus	oesophagus
6	chr16:11946600-11966800	Weak transcription	Lung	lung
7	chr16:11946600-11969000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:11946600-11970400	Weak transcription	Right Atrium	heart
9	chr16:11947000-11969400	Weak transcription	Right Ventricle	heart
10	chr16:11947200-11966800	Weak transcription	Small Intestine	intestine
11	chr16:11947200-11967200	Weak transcription	Fetal Intestine Small	intestine
12	chr16:11947200-11967200	Weak transcription	Fetal Stomach	stomach
13	chr16:11947200-11968800	Weak transcription	Ovary	ovary
14	chr16:11948000-11963400	Weak transcription	Spleen	Spleen
15	chr16:11948400-11963200	Weak transcription	Fetal Lung	lung
16	chr16:11948400-11969000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr16:11948600-11963200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:11948600-11969000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr16:11948800-11963400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr16:11948800-11965000	Weak transcription	Brain Substantia Nigra	brain
21	chr16:11948800-11965600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr16:11948800-11966200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr16:11948800-11966600	Weak transcription	Colon Smooth Muscle	Colon
24	chr16:11948800-11969400	Weak transcription	Brain Angular Gyrus	brain
25	chr16:11948800-11970200	Weak transcription	Gastric	stomach
26	chr16:11949600-11965600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr16:11956600-11965800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr16:11958400-11963400	Weak transcription	Brain Anterior Caudate	brain
29	chr16:11958400-11965400	Weak transcription	Fetal Heart	heart
30	chr16:11958800-11969200	Weak transcription	Psoas Muscle	Psoas
31	chr16:11959200-11966600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr16:11959400-11964400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr16:11959400-11969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr16:11959600-11966400	Weak transcription	Colonic Mucosa	Colon
35	chr16:11959800-11963800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr16:11960600-11969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:11960600-11969600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr16:11961200-11972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr16:11961400-11963400	Strong transcription	Fetal Kidney	kidney
40	chr16:11961400-11963800	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr16:11961400-11963800	Strong transcription	GM12878-XiMat	blood
42	chr16:11961400-11964600	Strong transcription	HSMM	muscle
43	chr16:11961400-11965400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr16:11961400-11966600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr16:11961400-11967000	Strong transcription	Primary T cells from cord blood	blood
46	chr16:11961400-11975600	Weak transcription	Pancreas	Pancrea
47	chr16:11961600-11963400	Weak transcription	K562	blood
48	chr16:11961600-11963800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr16:11961600-11966000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr16:11961600-11971600	Strong transcription	NHDF-Ad	bronchial

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