Variant report

Variant	rs6498261
Chromosome Location	chr16:12098857-12098858
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12070747..12072341-chr16:12096319..12098894,2	MCF-7	breast:
2	chr16:12090531..12092530-chr16:12098658..12100809,2	K562	blood:

Variant related genes	Relation type
ENSG00000260488	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10163386	0.83[ASN][1000 genomes]
rs11075041	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11639821	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11641950	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11644227	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11648938	0.83[MEX][hapmap]
rs11859213	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11859801	0.83[CHD][hapmap]
rs11862467	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13334063	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2865105	0.93[CEU][hapmap];0.83[CHD][hapmap]
rs3844112	0.89[CEU][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3916255	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs417938	0.86[MEX][hapmap]
rs442234	0.85[CHD][hapmap];0.82[MEX][hapmap]
rs59446863	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6498260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6498262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7197059	0.89[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7206768	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8044943	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8051012	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8051298	0.83[CHD][hapmap]
rs8060439	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8062691	0.87[MEX][hapmap]
rs9929844	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	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
2	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv984259	chr16:12092609-12104575	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6498261	TNFRSF17	cis	cerebellum	SCAN
rs6498261	RP11-166B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6498261	GSPT1	cis	parietal	SCAN
rs6498261	TNFRSF17	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071400-12130800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
3	chr16:12072200-12102600	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr16:12072400-12104400	Weak transcription	NHLF	lung
5	chr16:12072600-12099000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr16:12072800-12102800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:12079600-12109600	Weak transcription	Gastric	stomach
8	chr16:12083400-12102800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr16:12085400-12118200	Weak transcription	Esophagus	oesophagus
10	chr16:12088200-12100800	Weak transcription	Fetal Brain Female	brain
11	chr16:12088600-12104200	Weak transcription	Right Ventricle	heart
12	chr16:12088600-12109200	Weak transcription	Fetal Kidney	kidney
13	chr16:12088600-12110000	Weak transcription	NH-A	brain
14	chr16:12088800-12106600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr16:12088800-12108200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr16:12088800-12115400	Weak transcription	Placenta	Placenta
17	chr16:12089000-12099800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr16:12089000-12104400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr16:12089400-12103000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr16:12091000-12103000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr16:12091400-12103000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr16:12091800-12101200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr16:12092400-12105600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr16:12092400-12110200	Weak transcription	NHEK	skin
25	chr16:12092600-12107800	Weak transcription	Liver	Liver
26	chr16:12092800-12101200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr16:12093200-12101600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr16:12093200-12103800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr16:12093400-12102000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr16:12093400-12104000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:12093800-12103400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr16:12094000-12103000	Weak transcription	Brain Substantia Nigra	brain
33	chr16:12094200-12100800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr16:12094200-12103800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr16:12094200-12105600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr16:12094200-12110000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:12094800-12103000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr16:12094800-12103000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr16:12094800-12104200	Weak transcription	Left Ventricle	heart
40	chr16:12095000-12103800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:12096400-12099800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr16:12096400-12099800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr16:12096400-12101000	Strong transcription	Primary B cells from cord blood	blood
44	chr16:12096600-12099600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr16:12096800-12099800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr16:12096800-12099800	Strong transcription	Lung	lung
47	chr16:12096800-12100200	Weak transcription	Fetal Heart	heart
48	chr16:12096800-12101400	Weak transcription	HSMMtube	muscle
49	chr16:12096800-12103800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr16:12096800-12104000	Weak transcription	NHDF-Ad	bronchial

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