Variant report

Variant	rs12921440
Chromosome Location	chr16:30408765-30408766
allele	C/T
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:11)
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	GATA2	chr16:30408310-30408765	K562	blood:	n/a	chr16:30408598-30408608 chr16:30408587-30408604 chr16:30408596-30408605
2	TEAD4	chr16:30408304-30408766	K562	blood:	n/a	n/a
3	RCOR1	chr16:30408428-30408769	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30407328..30409721-chr16:30430312..30432675,2	MCF-7	breast:
2	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
3	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
4	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
5	chr16:30407687..30410209-chr16:30656586..30658459,2	MCF-7	breast:
6	chr16:30401749..30403997-chr16:30408377..30410909,4	K562	blood:
7	chr16:30378819..30383918-chr16:30407597..30413128,8	MCF-7	breast:
8	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:
9	chr16:30061476..30064810-chr16:30408529..30411930,3	MCF-7	breast:
10	chr16:30366042..30367681-chr16:30406512..30408947,2	MCF-7	breast:
11	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:

No data

Variant related genes	Relation type
SEPT1	TF binding region
ENSG00000199787	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000270466	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000149926	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000149925	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11150586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11646130	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11862806	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11863150	0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12446288	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12447833	0.92[ASN][1000 genomes]
rs12929884	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs13333093	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35480350	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs35598865	1.00[JPT][hapmap]
rs3574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340343	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4465620	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4787642	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4787643	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs4788409	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs4788413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788414	0.82[EUR][1000 genomes]
rs62055459	0.90[ASN][1000 genomes]
rs6565182	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6565183	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs7203359	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8046445	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8049108	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs8050812	1.00[JPT][hapmap]
rs8051096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8060853	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888967	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking 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	37 gene(s)	inside rSNPs	diseases
9	nsv1782	chr16:30391812-30410266	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12921440	MAPK3	cis	parietal	SCAN
rs12921440	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs12921440	TBX6	cis	parietal	SCAN
rs12921440	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30407600-30408800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:30407600-30408800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:30407600-30408800	Weak transcription	Gastric	stomach
4	chr16:30407600-30408800	Weak transcription	Pancreas	Pancrea
5	chr16:30407600-30409200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:30407600-30409200	Weak transcription	Aorta	Aorta
7	chr16:30407600-30411000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr16:30407600-30411400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr16:30407800-30408800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr16:30407800-30408800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr16:30407800-30408800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr16:30407800-30408800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr16:30407800-30408800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr16:30407800-30408800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr16:30407800-30408800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:30407800-30408800	Enhancers	Fetal Heart	heart
17	chr16:30407800-30408800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr16:30407800-30408800	Weak transcription	HSMMtube	muscle
19	chr16:30407800-30409000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr16:30407800-30409000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr16:30407800-30409000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr16:30407800-30409000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr16:30407800-30409200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr16:30407800-30409200	Weak transcription	Adipose Nuclei	Adipose
25	chr16:30407800-30409200	Enhancers	Stomach Mucosa	stomach
26	chr16:30407800-30410800	Weak transcription	HSMM	muscle
27	chr16:30407800-30410800	Weak transcription	NHDF-Ad	bronchial
28	chr16:30407800-30411000	Weak transcription	Fetal Kidney	kidney
29	chr16:30407800-30411200	Weak transcription	Psoas Muscle	Psoas
30	chr16:30408000-30408800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr16:30408000-30408800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr16:30408000-30408800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr16:30408000-30408800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr16:30408000-30408800	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:30408000-30408800	Weak transcription	Right Ventricle	heart
36	chr16:30408000-30408800	Enhancers	Stomach Smooth Muscle	stomach
37	chr16:30408000-30409000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr16:30408000-30409000	Genic enhancers	Fetal Thymus	thymus
39	chr16:30408000-30409000	Weak transcription	NHLF	lung
40	chr16:30408000-30409000	Weak transcription	Osteobl	bone
41	chr16:30408000-30409200	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr16:30408000-30410000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr16:30408000-30410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr16:30408000-30410600	Weak transcription	NH-A	brain
45	chr16:30408000-30410800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr16:30408000-30410800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr16:30408000-30411000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:30408000-30411000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr16:30408000-30411000	Weak transcription	Brain Angular Gyrus	brain
50	chr16:30408000-30411000	Weak transcription	Brain Substantia Nigra	brain

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