Variant report

Variant	rs12920172
Chromosome Location	chr16:81361544-81361545
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81298425..81302121-chr16:81361527..81366002,4	MCF-7	breast:
2	chr16:81311019..81313115-chr16:81360048..81362169,2	MCF-7	breast:
3	chr16:81359720..81362731-chr16:81363327..81365918,3	MCF-7	breast:
4	chr16:81358702..81362075-chr16:81365943..81367712,3	K562	blood:
5	chr16:81303770..81306348-chr16:81361148..81363746,2	MCF-7	breast:
6	chr16:81069397..81071026-chr16:81361127..81363315,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1035572	0.83[GIH][hapmap]
rs11150382	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11150383	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11639818	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11641053	0.81[GIH][hapmap]
rs11641889	0.81[CEU][hapmap]
rs11860448	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12103052	0.84[CHD][hapmap];0.81[YRI][hapmap]
rs12445484	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12447470	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12448813	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs12918775	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12921222	0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12927652	0.86[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12929924	0.86[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap]
rs12933277	0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12934500	0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap]
rs1564116	0.85[YRI][hapmap]
rs16955063	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1820260	0.86[CHB][hapmap]
rs2216768	0.89[CEU][hapmap]
rs7194094	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap]
rs7196957	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7196981	0.89[CEU][hapmap];0.83[GIH][hapmap]
rs7197360	0.86[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7202734	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7203482	0.86[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs8051314	1.00[YRI][hapmap]
rs8062704	0.85[CEU][hapmap];0.95[GIH][hapmap];0.84[EUR][1000 genomes]
rs9921359	0.85[CHD][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs9922086	0.81[CHD][hapmap]
rs9934557	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9938148	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1058519	chr16:81177767-81735333	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv948448	chr16:81198147-81906766	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases
5	nsv1061359	chr16:81349826-81471867	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
6	nsv542992	chr16:81349826-81471867	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
7	nsv524477	chr16:81359467-81362134	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv524464	chr16:81359467-81365974	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81349800-81365800	Weak transcription	Aorta	Aorta
2	chr16:81350000-81361600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr16:81350000-81364800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:81350000-81365800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr16:81350000-81371200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr16:81350000-81372000	Weak transcription	Primary B cells from cord blood	blood
7	chr16:81350000-81373200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr16:81350000-81375000	Weak transcription	Fetal Intestine Large	intestine
9	chr16:81350400-81367600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr16:81350400-81370400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr16:81350400-81373200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr16:81350600-81363000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr16:81350600-81367600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr16:81350600-81372800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr16:81350800-81365800	Weak transcription	Fetal Brain Male	brain
16	chr16:81351200-81369800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr16:81351400-81368800	Weak transcription	Dnd41	blood
18	chr16:81351400-81371200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr16:81352600-81362800	Weak transcription	Gastric	stomach
20	chr16:81352800-81366000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr16:81352800-81367400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr16:81353200-81367800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr16:81353400-81373200	Weak transcription	HUVEC	blood vessel
24	chr16:81353400-81390400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr16:81353600-81366200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:81353800-81372600	Weak transcription	A549	lung
27	chr16:81354000-81361800	Weak transcription	HSMMtube	muscle
28	chr16:81354000-81364600	Weak transcription	Small Intestine	intestine
29	chr16:81354000-81371400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr16:81354200-81391600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:81354400-81372800	Weak transcription	HSMM	muscle
32	chr16:81354600-81361800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr16:81355600-81371600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr16:81355800-81362400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:81357800-81361600	Enhancers	Brain Anterior Caudate	brain
36	chr16:81357800-81375800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr16:81358600-81362800	Weak transcription	Left Ventricle	heart
38	chr16:81358600-81367400	Weak transcription	Right Ventricle	heart
39	chr16:81358800-81362800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr16:81358800-81363600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr16:81358800-81365800	Weak transcription	Fetal Intestine Small	intestine
42	chr16:81358800-81365800	Weak transcription	Fetal Stomach	stomach
43	chr16:81358800-81367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr16:81358800-81369600	Weak transcription	K562	blood
45	chr16:81358800-81372200	Weak transcription	Right Atrium	heart
46	chr16:81358800-81372400	Weak transcription	Lung	lung
47	chr16:81359000-81369400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr16:81359000-81370000	Weak transcription	HepG2	liver
49	chr16:81359200-81363400	Weak transcription	Esophagus	oesophagus
50	chr16:81359200-81366000	Weak transcription	Brain Cingulate Gyrus	brain

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