Variant report

Variant	rs1703492
Chromosome Location	chr16:12136954-12136955
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11648938	0.91[MEX][hapmap]
rs12922317	0.91[CEU][hapmap]
rs1616017	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616090	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1641835	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641838	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs168409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168411	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1703493	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1703494	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs171222	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2541581	0.80[ASN][1000 genomes]
rs2541582	0.81[ASN][1000 genomes]
rs2541583	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2541584	0.82[AMR][1000 genomes]
rs2662829	0.86[CHB][hapmap]
rs2662830	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350214	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs350215	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs350216	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs350218	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs350220	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350221	0.90[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs350222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3851005	0.87[CEU][hapmap]
rs7192491	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8043644	0.91[CEU][hapmap]
rs8050827	0.82[MEX][hapmap]
rs8055073	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8061496	0.91[CEU][hapmap]
rs8062691	0.87[MEX][hapmap]
rs959665	0.83[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	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
2	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
3	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
4	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
5	nsv977110	chr16:12123355-12146787	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1703492	TNFRSF17	cis	cerebellum	SCAN
rs1703492	GSPT1	cis	parietal	SCAN
rs1703492	TNFRSF17	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12071800-12140200	Weak transcription	Fetal Intestine Small	intestine
2	chr16:12099600-12141200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr16:12105200-12142200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr16:12109800-12142200	Weak transcription	Gastric	stomach
5	chr16:12112000-12142200	Weak transcription	NHLF	lung
6	chr16:12112000-12144000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr16:12115200-12140600	Weak transcription	Thymus	Thymus
8	chr16:12116200-12141000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr16:12117200-12140400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr16:12117400-12183400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr16:12118200-12140400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr16:12119200-12146400	Weak transcription	Fetal Lung	lung
13	chr16:12119400-12142000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr16:12119600-12148400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr16:12121000-12142200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr16:12121400-12155000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr16:12121600-12140200	Weak transcription	Fetal Thymus	thymus
18	chr16:12121600-12142000	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr16:12121800-12140000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr16:12122200-12140200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr16:12122200-12140800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:12122800-12144000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr16:12124400-12156600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr16:12124800-12142000	Weak transcription	Esophagus	oesophagus
25	chr16:12124800-12155000	Weak transcription	NH-A	brain
26	chr16:12125000-12140200	Weak transcription	Lung	lung
27	chr16:12126400-12150000	Weak transcription	Small Intestine	intestine
28	chr16:12130000-12139800	Weak transcription	Liver	Liver
29	chr16:12130000-12142200	Weak transcription	Brain Angular Gyrus	brain
30	chr16:12130000-12153000	Weak transcription	Ovary	ovary
31	chr16:12130200-12142000	Weak transcription	Aorta	Aorta
32	chr16:12131000-12141600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr16:12131000-12142200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr16:12131200-12139800	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:12131200-12139800	Weak transcription	Right Ventricle	heart
36	chr16:12131200-12140200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr16:12131200-12140600	Weak transcription	Fetal Muscle Leg	muscle
38	chr16:12131200-12141000	Weak transcription	GM12878-XiMat	blood
39	chr16:12131200-12142200	Weak transcription	Brain Anterior Caudate	brain
40	chr16:12131200-12142200	Weak transcription	Brain Substantia Nigra	brain
41	chr16:12131200-12142200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr16:12131200-12142200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr16:12131200-12144000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr16:12131200-12153000	Weak transcription	Right Atrium	heart
45	chr16:12131200-12156600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:12131400-12140400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr16:12131400-12140800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr16:12131400-12148200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr16:12131400-12150800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr16:12131400-12150800	Weak transcription	HSMMtube	muscle

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