Variant report

Variant	rs4889620
Chromosome Location	chr16:31131174-31131175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31127491..31131830-chr16:31190393..31192870,6	MCF-7	breast:
2	chr16:31127220..31133615-chr16:31189948..31195209,18	K562	blood:
3	chr16:31104440..31108567-chr16:31128079..31131886,5	MCF-7	breast:
4	chr16:30816280..30819245-chr16:31129948..31132814,2	K562	blood:
5	chr16:30966438..30967999-chr16:31130219..31132345,2	K562	blood:
6	chr16:31129797..31131930-chr17:56707897..56709423,2	MCF-7	breast:
7	chr16:30968063..30971621-chr16:31128915..31132343,4	K562	blood:

Variant related genes	Relation type
ENSG00000255439	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000260304	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000167397	Chromatin interaction
ENSG00000099381	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

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	0.94[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	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12716981	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716982	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12934418	0.84[ASN][1000 genomes]
rs14235	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549293	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17839567	0.84[ASN][1000 genomes]
rs17839568	0.95[ASN][1000 genomes]
rs1978485	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978487	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032915	0.89[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	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2855475	0.88[AMR][1000 genomes];1.00[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	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889530	0.82[ASN][1000 genomes]
rs4889619	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55766044	1.00[ASN][1000 genomes]
rs55979739	0.84[ASN][1000 genomes]
rs56284083	0.84[ASN][1000 genomes]
rs56314408	0.90[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	0.89[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	0.89[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	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs749671	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs749767	0.81[AMR][1000 genomes];0.94[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	0.95[ASN][1000 genomes]
rs8056842	0.84[ASN][1000 genomes]
rs8061047	0.89[ASN][1000 genomes]
rs881929	0.95[ASN][1000 genomes]
rs889548	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889555	1.00[ASN][1000 genomes]
rs9923231	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9925964	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9929899	0.82[ASN][1000 genomes]
rs9934438	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9936329	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939417	0.84[ASN][1000 genomes]
rs9939558	0.84[ASN][1000 genomes]
rs9972727	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4889620	RP11-196G11.2	cis	Muscle Skeletal	GTEx
rs4889620	KAT8	cis	Artery Tibial	GTEx
rs4889620	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs4889620	HSD3B7	cis	Whole Blood	GTEx
rs4889620	KAT8	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31129800-31131200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr16:31129800-31131400	Weak transcription	Esophagus	oesophagus
3	chr16:31129800-31131400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:31130000-31131400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:31130000-31131400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:31130000-31131400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr16:31130000-31131400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:31130000-31131400	Weak transcription	Aorta	Aorta
9	chr16:31130000-31131800	Genic enhancers	Pancreas	Pancrea
10	chr16:31130000-31132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr16:31130200-31131200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr16:31130200-31131200	Genic enhancers	Primary monocytes fromperipheralblood	blood
13	chr16:31130200-31131200	Enhancers	Psoas Muscle	Psoas
14	chr16:31130200-31131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr16:31130200-31131400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr16:31130200-31131400	Weak transcription	HUVEC	blood vessel
17	chr16:31130200-31133800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr16:31130200-31133800	Strong transcription	Brain Germinal Matrix	brain
19	chr16:31130200-31134000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:31130200-31135600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:31130200-31136600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr16:31130400-31131200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr16:31130400-31131200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr16:31130400-31131200	Weak transcription	Gastric	stomach
25	chr16:31130400-31131200	Weak transcription	Spleen	Spleen
26	chr16:31130400-31131200	Weak transcription	HepG2	liver
27	chr16:31130400-31131400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr16:31130400-31131400	Weak transcription	Brain Angular Gyrus	brain
29	chr16:31130400-31131400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr16:31130400-31131400	Weak transcription	Brain Substantia Nigra	brain
31	chr16:31130400-31131400	Weak transcription	Colon Smooth Muscle	Colon
32	chr16:31130400-31131400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr16:31130400-31131400	Weak transcription	Fetal Brain Male	brain
34	chr16:31130400-31131400	Weak transcription	Fetal Kidney	kidney
35	chr16:31130400-31131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr16:31130400-31131400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr16:31130400-31131400	Weak transcription	Right Ventricle	heart
38	chr16:31130400-31131400	Weak transcription	Small Intestine	intestine
39	chr16:31130400-31131400	Weak transcription	A549	lung
40	chr16:31130400-31131400	Weak transcription	GM12878-XiMat	blood
41	chr16:31130400-31131400	Weak transcription	HSMM	muscle
42	chr16:31130400-31131400	Weak transcription	HSMMtube	muscle
43	chr16:31130400-31131400	Weak transcription	NH-A	brain
44	chr16:31130400-31131600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr16:31130400-31133800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr16:31130400-31133800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr16:31130400-31134200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr16:31130400-31134400	Strong transcription	Fetal Lung	lung
49	chr16:31130400-31135800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr16:31130400-31137200	Weak transcription	Stomach Mucosa	stomach

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