Variant report

Variant	rs12926295
Chromosome Location	chr16:30890538-30890539
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:30890445-30890694	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30890237..30893822-chr16:30910547..30914348,3	MCF-7	breast:
2	chr16:30885063..30889617-chr16:30890283..30895717,8	K562	blood:
3	chr16:30890209..30891734-chr16:30905401..30907788,2	K562	blood:
4	chr16:30888368..30890823-chr16:30895784..30897904,3	K562	blood:

Variant related genes	Relation type
MIR4519	TF binding region
ENSG00000099385	Chromatin interaction
ENSG00000262721	Chromatin interaction
ENSG00000265991	Chromatin interaction
ENSG00000260083	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1046276	0.91[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs10782001	0.91[CEU][hapmap]
rs10782002	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs10871454	0.88[JPT][hapmap]
rs11076	0.81[CEU][hapmap]
rs11150596	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs11150599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11150600	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs11150601	0.92[CHD][hapmap]
rs11150604	0.88[JPT][hapmap]
rs11640534	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs11640961	0.92[CHD][hapmap]
rs11647697	0.89[ASN][1000 genomes]
rs11649653	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs11862744	0.88[JPT][hapmap]
rs11862962	0.92[ASN][1000 genomes]
rs11864054	0.82[CHB][hapmap]
rs12445650	0.86[JPT][hapmap]
rs12920259	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12924903	0.91[CEU][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs12926237	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12928081	0.95[ASN][1000 genomes]
rs12928852	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs12929065	0.89[ASN][1000 genomes]
rs12930545	0.87[CEU][hapmap];0.84[CHD][hapmap]
rs12930944	0.89[ASN][1000 genomes]
rs12931046	0.92[CHD][hapmap]
rs1458201	0.84[CHD][hapmap]
rs1458202	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs1870293	0.92[CHD][hapmap]
rs2054213	0.92[CHD][hapmap]
rs2125293	0.89[ASN][1000 genomes]
rs2168834	0.89[ASN][1000 genomes]
rs2303222	0.88[JPT][hapmap]
rs2303223	0.88[JPT][hapmap]
rs2305880	0.92[CHD][hapmap]
rs2305884	0.92[CHD][hapmap]
rs2335013	0.89[ASN][1000 genomes]
rs2878304	0.97[ASN][1000 genomes]
rs35468353	0.88[JPT][hapmap]
rs35675346	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs3813020	0.86[CEU][hapmap];0.92[CHD][hapmap]
rs4290486	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889490	0.82[CHB][hapmap]
rs4889525	0.92[CHD][hapmap]
rs4889534	0.89[ASN][1000 genomes]
rs4889536	0.89[ASN][1000 genomes]
rs4889599	0.92[CHD][hapmap]
rs4889603	0.92[CHD][hapmap]
rs4889604	0.92[CHD][hapmap]
rs4889609	0.88[JPT][hapmap]
rs4889614	0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4889622	0.89[ASN][1000 genomes]
rs4889627	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4889630	1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4889634	0.86[ASN][1000 genomes]
rs4889651	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4889653	1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55719146	0.92[ASN][1000 genomes]
rs56083427	0.97[ASN][1000 genomes]
rs6565217	0.88[JPT][hapmap]
rs67264578	0.95[ASN][1000 genomes]
rs67456613	0.97[ASN][1000 genomes]
rs7197717	0.88[JPT][hapmap]
rs7200879	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs7204459	0.92[CHD][hapmap]
rs7206511	0.91[CEU][hapmap];0.92[CHD][hapmap]
rs72799330	0.92[ASN][1000 genomes]
rs729482	0.88[JPT][hapmap]
rs732172	0.88[JPT][hapmap]
rs749670	0.86[JPT][hapmap]
rs749671	0.88[JPT][hapmap]
rs7500719	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs8046001	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs8046391	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs8046707	0.92[CHD][hapmap]
rs8050107	0.92[ASN][1000 genomes]
rs8050588	0.91[CEU][hapmap]
rs8056842	0.88[JPT][hapmap]
rs8058961	0.82[CHB][hapmap]
rs8060857	0.92[CHD][hapmap]
rs8062719	0.92[CHD][hapmap]
rs8063565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs881929	0.88[JPT][hapmap]
rs897984	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897986	0.92[CHD][hapmap]
rs9319588	0.91[CEU][hapmap]
rs9932572	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9933843	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9938550	0.84[CHD][hapmap]
rs9939417	0.88[JPT][hapmap]

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	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	nsv905728	chr16:30642867-30928970	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	171 gene(s)	inside rSNPs	diseases
5	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
6	esv1825223	chr16:30669091-30971810	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
7	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
8	nsv905733	chr16:30796919-31004812	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	112 gene(s)	inside rSNPs	diseases
9	nsv869652	chr16:30799471-30951038	Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833189	chr16:30819708-30960795	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	79 gene(s)	inside rSNPs	diseases
11	nsv833190	chr16:30845051-31007863	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
12	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
13	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
14	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12926295	HSD3B7	cis	Esophagus Mucosa	GTEx
rs12926295	MYST1	cis	parietal	SCAN
rs12926295	ZNF785	cis	lymphoblastoid	seeQTL
rs12926295	PHKG2	cis	parietal	SCAN
rs12926295	MYST1	cis	cerebellum	SCAN
rs12926295	ITGAX	cis	parietal	SCAN
rs12926295	RABEP2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30887600-30893800	Weak transcription	Aorta	Aorta
2	chr16:30887600-30896200	Weak transcription	Ovary	ovary
3	chr16:30888400-30890600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr16:30888400-30890600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr16:30888400-30891200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr16:30888400-30892400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr16:30888400-30892800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr16:30888400-30892800	Weak transcription	NHLF	lung
9	chr16:30888400-30893000	Weak transcription	Right Atrium	heart
10	chr16:30888400-30893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:30888400-30893600	Weak transcription	NH-A	brain
12	chr16:30888400-30894200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr16:30888400-30894200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr16:30888400-30894400	Weak transcription	K562	blood
15	chr16:30888400-30895600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:30888400-30896000	Weak transcription	HSMM	muscle
17	chr16:30888400-30896200	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:30888400-30896200	Weak transcription	Gastric	stomach
19	chr16:30888400-30896200	Weak transcription	HSMMtube	muscle
20	chr16:30888400-30896200	Weak transcription	NHEK	skin
21	chr16:30888400-30896600	Weak transcription	Fetal Kidney	kidney
22	chr16:30888400-30896800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr16:30888400-30897200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr16:30888400-30899000	Weak transcription	HMEC	breast
25	chr16:30888400-30899200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:30888400-30900000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr16:30888400-30900000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:30888400-30900000	Weak transcription	NHDF-Ad	bronchial
29	chr16:30888400-30900200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr16:30888400-30900200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:30888400-30900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:30888400-30903800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr16:30888400-30903800	Strong transcription	Fetal Stomach	stomach
34	chr16:30888400-30904000	Weak transcription	Stomach Mucosa	stomach
35	chr16:30888400-30904000	Weak transcription	HUVEC	blood vessel
36	chr16:30888400-30904200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr16:30888400-30904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr16:30888400-30904400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:30888600-30891400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr16:30888600-30892800	Strong transcription	Fetal Intestine Small	intestine
41	chr16:30888600-30893600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr16:30888600-30893600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr16:30888600-30893600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr16:30888600-30894200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr16:30888600-30894200	Weak transcription	Fetal Heart	heart
46	chr16:30888600-30896200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr16:30888600-30904000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:30888600-30904000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr16:30888600-30904000	Weak transcription	Colon Smooth Muscle	Colon
50	chr16:30888800-30891600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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