Variant report

Variant	rs11642003
Chromosome Location	chr16:31068391-31068392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1108431	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11640767	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11640957	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11647284	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11864806	0.82[ASN][1000 genomes]
rs11864839	0.82[ASN][1000 genomes]
rs11865038	0.82[ASN][1000 genomes]
rs17839568	0.82[ASN][1000 genomes]
rs2303222	0.82[ASN][1000 genomes]
rs2303223	0.84[ASN][1000 genomes]
rs2359612	0.82[ASN][1000 genomes]
rs28814987	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34649473	0.81[ASN][1000 genomes]
rs35351013	0.89[ASN][1000 genomes]
rs35713203	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3751855	0.82[ASN][1000 genomes]
rs4468641	0.82[ASN][1000 genomes]
rs4889530	0.82[ASN][1000 genomes]
rs55979739	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56813533	0.89[ASN][1000 genomes]
rs57434408	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59061704	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61162043	0.82[ASN][1000 genomes]
rs6565217	0.82[ASN][1000 genomes]
rs7196161	0.82[ASN][1000 genomes]
rs7196726	0.82[ASN][1000 genomes]
rs7197717	0.82[ASN][1000 genomes]
rs7199949	0.82[ASN][1000 genomes]
rs7294	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs732172	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs732173	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73530203	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs749670	0.82[ASN][1000 genomes]
rs749671	0.82[ASN][1000 genomes]
rs750952	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8047803	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8050894	0.82[ASN][1000 genomes]
rs8061047	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs881929	0.82[ASN][1000 genomes]
rs9923231	0.82[ASN][1000 genomes]
rs9934438	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
13	nsv827614	chr16:31058322-31072059	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv905740	chr16:31066249-31232437	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases
15	nsv905741	chr16:31066249-31247924	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	202 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11642003	STX1B	cis	Thyroid	GTEx
rs11642003	RP11-196G11.2	cis	Esophagus Muscularis	GTEx
rs11642003	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs11642003	STX4	Cis_1M	lymphoblastoid	RTeQTL
rs11642003	MYST1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31046000-31071000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31046000-31083200	Weak transcription	Right Atrium	heart
3	chr16:31048200-31071400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr16:31049600-31075600	Weak transcription	Psoas Muscle	Psoas
5	chr16:31051200-31071000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr16:31051400-31083000	Weak transcription	Fetal Lung	lung
7	chr16:31052000-31071800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr16:31052000-31083400	Weak transcription	Primary B cells from cord blood	blood
9	chr16:31052400-31074400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr16:31053800-31072000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr16:31054000-31069200	Weak transcription	Fetal Brain Female	brain
12	chr16:31054000-31072600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:31054000-31083200	Weak transcription	Fetal Kidney	kidney
14	chr16:31054200-31071000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr16:31054200-31076200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr16:31054400-31071800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr16:31054400-31072000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr16:31054600-31071600	Weak transcription	Dnd41	blood
19	chr16:31054600-31071800	Weak transcription	GM12878-XiMat	blood
20	chr16:31054600-31072000	Weak transcription	Esophagus	oesophagus
21	chr16:31054600-31072200	Weak transcription	Colonic Mucosa	Colon
22	chr16:31054800-31068800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr16:31054800-31069000	Weak transcription	Thymus	Thymus
24	chr16:31054800-31069200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr16:31054800-31071000	Weak transcription	Fetal Thymus	thymus
26	chr16:31054800-31071400	Weak transcription	Brain Hippocampus Middle	brain
27	chr16:31054800-31071600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr16:31054800-31071600	Weak transcription	Gastric	stomach
29	chr16:31054800-31071800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr16:31054800-31071800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr16:31054800-31071800	Weak transcription	Adipose Nuclei	Adipose
32	chr16:31054800-31071800	Weak transcription	Brain Germinal Matrix	brain
33	chr16:31054800-31072000	Weak transcription	Brain Anterior Caudate	brain
34	chr16:31054800-31072000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr16:31054800-31072000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr16:31054800-31072200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr16:31054800-31072200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:31054800-31072200	Weak transcription	Right Ventricle	heart
39	chr16:31054800-31072400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr16:31054800-31072400	Weak transcription	Aorta	Aorta
41	chr16:31054800-31072600	Weak transcription	Brain Substantia Nigra	brain
42	chr16:31055000-31069000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr16:31055000-31069200	Weak transcription	Lung	lung
44	chr16:31055000-31071000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr16:31055000-31071600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr16:31055000-31072000	Weak transcription	Ovary	ovary
47	chr16:31055000-31072000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr16:31055000-31072200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr16:31055000-31072200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr16:31055200-31071800	Weak transcription	Primary T cells from cord blood	blood

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