Variant report

Variant	rs12716981
Chromosome Location	chr16:31118024-31118025
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:31117900-31118050	AG04449	skin:	n/a	n/a
2	POLR2A	chr16:31103667-31119079	K562	blood:	n/a	n/a
3	POLR2A	chr16:31117739-31118074	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31117975..31125175-chr16:31188698..31192934,10	MCF-7	breast:
2	chr16:30996951..30999220-chr16:31117485..31119615,2	K562	blood:
3	chr16:31104528..31108651-chr16:31117626..31121071,4	MCF-7	breast:
4	chr16:31115598..31118169-chr16:31120150..31122491,2	K562	blood:
5	chr16:31117662..31120413-chr16:31270812..31272683,2	MCF-7	breast:
6	chr16:30960093..30962910-chr16:31117078..31118783,2	K562	blood:
7	chr16:31117883..31120430-chr16:31468936..31471435,2	MCF-7	breast:
8	chr16:31117742..31119780-chr16:31197007..31199693,2	MCF-7	breast:
9	chr16:31117735..31121210-chr16:31190065..31193528,11	K562	blood:

No data

Variant related genes	Relation type
BCKDK	TF binding region
ENSG00000252809	TF binding region
ENSG00000260267	Chromatin interaction
ENSG00000268863	Chromatin interaction
ENSG00000169896	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000255439	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000103507	Chromatin interaction
ENSG00000167397	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000252809	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1060506	1.00[ASN][1000 genomes]
rs10871454	0.80[ASN][1000 genomes]
rs1108431	0.84[ASN][1000 genomes]
rs11150604	0.84[ASN][1000 genomes]
rs11640767	0.82[ASN][1000 genomes]
rs11640957	0.82[ASN][1000 genomes]
rs11642192	0.93[ASN][1000 genomes]
rs11647284	0.95[ASN][1000 genomes]
rs11647442	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11862744	0.84[ASN][1000 genomes]
rs11864806	0.95[ASN][1000 genomes]
rs11864839	0.95[ASN][1000 genomes]
rs11865038	0.95[ASN][1000 genomes]
rs11865499	1.00[ASN][1000 genomes]
rs12445650	0.84[ASN][1000 genomes]
rs12448321	0.84[ASN][1000 genomes]
rs12597511	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12716982	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934418	0.84[ASN][1000 genomes]
rs14235	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549293	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839567	0.84[ASN][1000 genomes]
rs17839568	0.95[ASN][1000 genomes]
rs1978485	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978487	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032915	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288004	0.84[ASN][1000 genomes]
rs2303222	0.95[ASN][1000 genomes]
rs2303223	0.93[ASN][1000 genomes]
rs2359612	0.95[ASN][1000 genomes]
rs2855475	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28725459	0.96[ASN][1000 genomes]
rs28814987	0.95[ASN][1000 genomes]
rs2884738	1.00[ASN][1000 genomes]
rs34649473	0.81[ASN][1000 genomes]
rs35351013	0.89[ASN][1000 genomes]
rs35468353	0.84[ASN][1000 genomes]
rs35713203	0.95[ASN][1000 genomes]
rs3751855	0.95[ASN][1000 genomes]
rs4468641	0.95[ASN][1000 genomes]
rs4527034	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889530	0.82[ASN][1000 genomes]
rs4889619	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4889620	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55766044	1.00[ASN][1000 genomes]
rs55979739	0.84[ASN][1000 genomes]
rs56284083	0.84[ASN][1000 genomes]
rs56314408	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56813533	0.89[ASN][1000 genomes]
rs57434408	0.86[ASN][1000 genomes]
rs58726213	0.82[ASN][1000 genomes]
rs59061704	0.82[ASN][1000 genomes]
rs59735493	1.00[ASN][1000 genomes]
rs60996860	0.96[ASN][1000 genomes]
rs61162043	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61320757	1.00[ASN][1000 genomes]
rs6565217	0.95[ASN][1000 genomes]
rs7187995	0.89[ASN][1000 genomes]
rs7196161	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7196726	0.95[ASN][1000 genomes]
rs7197717	0.95[ASN][1000 genomes]
rs7199949	0.95[ASN][1000 genomes]
rs7294	0.95[ASN][1000 genomes]
rs732172	0.84[ASN][1000 genomes]
rs732173	0.84[ASN][1000 genomes]
rs73530203	0.93[ASN][1000 genomes]
rs749670	0.95[ASN][1000 genomes]
rs749671	0.95[ASN][1000 genomes]
rs749767	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7500176	0.84[ASN][1000 genomes]
rs750952	0.95[ASN][1000 genomes]
rs8047803	0.95[ASN][1000 genomes]
rs8050894	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8056842	0.84[ASN][1000 genomes]
rs8061047	0.89[ASN][1000 genomes]
rs881929	0.95[ASN][1000 genomes]
rs889548	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889555	1.00[ASN][1000 genomes]
rs9923231	0.95[ASN][1000 genomes]
rs9925964	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929899	0.82[ASN][1000 genomes]
rs9934438	0.95[ASN][1000 genomes]
rs9936329	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939417	0.84[ASN][1000 genomes]
rs9939558	0.84[ASN][1000 genomes]
rs9972727	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv905742	chr16:31102321-31247924	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	188 gene(s)	inside rSNPs	diseases
14	nsv905743	chr16:31111064-31129942	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12716981	HSD3B7	cis	Whole Blood	GTEx
rs12716981	KAT8	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31112800-31119200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr16:31113000-31119400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr16:31114600-31119400	Weak transcription	Lung	lung
4	chr16:31116400-31119000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr16:31117400-31118600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:31117400-31118600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr16:31117400-31118800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr16:31117400-31118800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr16:31117400-31118800	Weak transcription	Brain Hippocampus Middle	brain
10	chr16:31117400-31118800	Enhancers	GM12878-XiMat	blood
11	chr16:31117400-31119000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:31117400-31119000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr16:31117400-31119000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr16:31117400-31119000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr16:31117400-31119000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr16:31117400-31119000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr16:31117400-31119000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr16:31117400-31119000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:31117400-31119000	Weak transcription	Brain Substantia Nigra	brain
20	chr16:31117400-31119000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr16:31117400-31119000	Weak transcription	Fetal Brain Male	brain
22	chr16:31117400-31119000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr16:31117400-31119000	Weak transcription	Spleen	Spleen
24	chr16:31117400-31119000	Weak transcription	A549	lung
25	chr16:31117400-31119200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr16:31117400-31119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr16:31117400-31119200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr16:31117400-31119200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr16:31117400-31119200	Weak transcription	Brain Angular Gyrus	brain
30	chr16:31117400-31119200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr16:31117400-31119200	Weak transcription	Colon Smooth Muscle	Colon
32	chr16:31117400-31119200	Weak transcription	Fetal Heart	heart
33	chr16:31117400-31119200	Weak transcription	Fetal Stomach	stomach
34	chr16:31117400-31119200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr16:31117400-31119200	Weak transcription	HMEC	breast
36	chr16:31117400-31119200	Weak transcription	HSMM	muscle
37	chr16:31117400-31119200	Weak transcription	HUVEC	blood vessel
38	chr16:31117400-31119200	Weak transcription	NH-A	brain
39	chr16:31117400-31119400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr16:31117400-31119400	Weak transcription	Primary B cells from cord blood	blood
41	chr16:31117400-31119400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr16:31117400-31119400	Weak transcription	Aorta	Aorta
43	chr16:31117400-31119400	Weak transcription	Esophagus	oesophagus
44	chr16:31117400-31119400	Weak transcription	Gastric	stomach
45	chr16:31117400-31119400	Weak transcription	Left Ventricle	heart
46	chr16:31117400-31119400	Weak transcription	Ovary	ovary
47	chr16:31117400-31119400	Weak transcription	Psoas Muscle	Psoas
48	chr16:31117400-31119400	Weak transcription	Right Atrium	heart
49	chr16:31117400-31119400	Weak transcription	Right Ventricle	heart
50	chr16:31117400-31119400	Weak transcription	Small Intestine	intestine

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