Variant report

Variant	rs1108431
Chromosome Location	chr16:31054607-31054608
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31043970..31045853-chr16:31053165..31057721,4	K562	blood:
2	chr16:31008264..31010102-chr16:31053957..31055799,2	MCF-7	breast:
3	chr16:30967392..30969268-chr16:31053446..31056130,2	MCF-7	breast:
4	chr16:31053220..31057176-chr16:31073803..31076480,4	MCF-7	breast:
5	chr16:31048921..31052492-chr16:31052504..31056345,6	MCF-7	breast:
6	chr16:31054525..31057827-chr16:31082936..31085986,4	MCF-7	breast:
7	chr16:31052766..31056260-chr16:31190387..31193096,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC135050.1-2	chr16:31053463-31054786	NONHSAT141840

No data

Variant related genes	Relation type
ENSG00000099365	Chromatin interaction
ENSG00000103496	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000099381	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1060506	0.84[ASN][1000 genomes]
rs10871454	0.95[ASN][1000 genomes]
rs11150604	1.00[ASN][1000 genomes]
rs11640767	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11640957	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11642003	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11642192	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11647284	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11647442	0.84[ASN][1000 genomes]
rs11862744	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11864806	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11864839	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11865038	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11865499	0.84[ASN][1000 genomes]
rs12445650	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448321	1.00[ASN][1000 genomes]
rs12597511	0.82[ASN][1000 genomes]
rs12716981	0.84[ASN][1000 genomes]
rs12716982	0.84[ASN][1000 genomes]
rs12934418	1.00[ASN][1000 genomes]
rs14235	0.84[ASN][1000 genomes]
rs1549293	0.84[ASN][1000 genomes]
rs17839567	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839568	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1978485	0.84[ASN][1000 genomes]
rs1978487	0.84[ASN][1000 genomes]
rs2032915	0.84[ASN][1000 genomes]
rs2288004	1.00[ASN][1000 genomes]
rs2303222	0.89[ASN][1000 genomes]
rs2303223	0.86[ASN][1000 genomes]
rs2359612	0.89[ASN][1000 genomes]
rs2855475	0.84[ASN][1000 genomes]
rs28725459	0.81[ASN][1000 genomes]
rs28814987	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2884738	0.84[ASN][1000 genomes]
rs34649473	0.83[ASN][1000 genomes]
rs34898535	0.87[ASN][1000 genomes]
rs35351013	0.82[ASN][1000 genomes]
rs35468353	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35713203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35961830	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3751855	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4468641	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4527034	0.84[ASN][1000 genomes]
rs4889526	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4889530	0.89[ASN][1000 genomes]
rs4889609	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4889620	0.84[ASN][1000 genomes]
rs55766044	0.84[ASN][1000 genomes]
rs55979739	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56284083	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56314408	0.84[ASN][1000 genomes]
rs56813533	0.82[ASN][1000 genomes]
rs57434408	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57576577	0.89[EUR][1000 genomes]
rs58726213	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59061704	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59735493	0.84[ASN][1000 genomes]
rs60996860	0.81[ASN][1000 genomes]
rs61162043	0.89[ASN][1000 genomes]
rs61320757	0.84[ASN][1000 genomes]
rs6565217	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7187995	0.82[ASN][1000 genomes]
rs7196161	0.89[ASN][1000 genomes]
rs7196726	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197717	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7199949	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72800847	0.80[EUR][1000 genomes]
rs7294	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs732172	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732173	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530203	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs749670	0.89[ASN][1000 genomes]
rs749671	0.89[ASN][1000 genomes]
rs749767	0.84[ASN][1000 genomes]
rs7500176	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750952	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8047803	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8050894	0.89[ASN][1000 genomes]
rs8056842	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8061047	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs881929	0.89[ASN][1000 genomes]
rs889548	0.84[ASN][1000 genomes]
rs889555	0.84[ASN][1000 genomes]
rs9673641	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9923231	0.89[ASN][1000 genomes]
rs9925964	0.84[ASN][1000 genomes]
rs9929899	0.98[ASN][1000 genomes]
rs9934438	0.89[ASN][1000 genomes]
rs9936329	0.84[ASN][1000 genomes]
rs9939417	1.00[ASN][1000 genomes]
rs9939558	1.00[ASN][1000 genomes]
rs9972727	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
7	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
8	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
9	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
10	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
11	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
12	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1108431	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs1108431	STX1B	cis	Thyroid	GTEx
rs1108431	STX4	Cis_1M	lymphoblastoid	RTeQTL
rs1108431	RP11-196G11.2	cis	Esophagus Muscularis	GTEx
rs1108431	RP11-196G11.2	cis	lung	GTEx
rs1108431	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs1108431	KAT8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31045600-31055800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31046000-31071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
4	chr16:31046200-31054800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr16:31046200-31054800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr16:31046200-31055000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr16:31046200-31055000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr16:31046200-31055000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr16:31046200-31055200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr16:31046200-31058200	Weak transcription	HUVEC	blood vessel
11	chr16:31046200-31063000	Weak transcription	Hela-S3	cervix
12	chr16:31046200-31063200	Weak transcription	HMEC	breast
13	chr16:31046400-31054800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr16:31046400-31055000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr16:31046400-31055000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr16:31046400-31055000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr16:31046600-31055000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr16:31046800-31054800	Strong transcription	Gastric	stomach
19	chr16:31046800-31055800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr16:31047800-31054800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr16:31048000-31055200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr16:31048200-31063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr16:31048200-31063400	Weak transcription	K562	blood
24	chr16:31048200-31071400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:31048400-31054800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:31048400-31061600	Weak transcription	NHDF-Ad	bronchial
27	chr16:31048600-31054800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr16:31048600-31055200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr16:31049000-31054800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr16:31049000-31054800	Strong transcription	Brain Anterior Caudate	brain
31	chr16:31049000-31054800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr16:31049000-31055000	Strong transcription	Lung	lung
33	chr16:31049000-31056200	Strong transcription	Left Ventricle	heart
34	chr16:31049200-31054800	Strong transcription	Adipose Nuclei	Adipose
35	chr16:31049200-31054800	Strong transcription	Right Ventricle	heart
36	chr16:31049200-31054800	Strong transcription	Thymus	Thymus
37	chr16:31049200-31055000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr16:31049200-31055000	Strong transcription	Liver	Liver
39	chr16:31049200-31055000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr16:31049400-31054800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr16:31049600-31057600	Weak transcription	Stomach Mucosa	stomach
42	chr16:31049600-31075600	Weak transcription	Psoas Muscle	Psoas
43	chr16:31051000-31055200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr16:31051000-31063200	Weak transcription	NH-A	brain
45	chr16:31051200-31071000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr16:31051400-31055400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr16:31051400-31083000	Weak transcription	Fetal Lung	lung
48	chr16:31051600-31054800	Strong transcription	Brain Hippocampus Middle	brain
49	chr16:31052000-31071800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr16:31052000-31083400	Weak transcription	Primary B cells from cord blood	blood

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