Variant report

Variant	rs4456350
Chromosome Location	chr12:124058489-124058490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:124056996..124059825-chr12:124068978..124071238,2	MCF-7	breast:
2	chr12:124056030..124058750-chr12:124059393..124062222,4	K562	blood:
3	chr12:124057277..124059073-chr12:124064975..124067218,3	MCF-7	breast:
4	chr12:124056886..124060484-chr12:124067247..124069927,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086598	Chromatin interaction
ENSG00000247373	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1051793	0.80[CEU][hapmap]
rs1060637	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs10846531	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs10846535	0.89[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10846537	0.85[CEU][hapmap]
rs11057307	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11572920	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs11572952	0.81[CEU][hapmap]
rs11609591	0.89[CEU][hapmap]
rs11611354	0.85[CEU][hapmap]
rs11612030	0.88[CEU][hapmap]
rs11612479	0.85[CEU][hapmap]
rs11612927	0.84[CEU][hapmap]
rs11613632	0.84[CEU][hapmap]
rs12817757	0.84[CEU][hapmap]
rs12820195	0.85[CEU][hapmap]
rs12821242	0.87[CEU][hapmap]
rs12827074	0.85[CEU][hapmap]
rs12829893	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs12830927	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs1515814	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1515815	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs2048802	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2222060	0.81[CEU][hapmap]
rs2250026	0.85[CEU][hapmap]
rs3748268	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs3748269	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4040225	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930708	0.85[CEU][hapmap]
rs6488883	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488888	0.81[CEU][hapmap]
rs6488893	0.85[CEU][hapmap]
rs6488897	0.89[CEU][hapmap]
rs6551	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133199	0.88[CEU][hapmap]
rs7134074	0.88[CEU][hapmap]
rs7134896	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135660	0.84[CEU][hapmap]
rs7136939	0.85[CEU][hapmap]
rs7137946	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs7139193	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs7294984	0.81[CEU][hapmap]
rs7297576	0.89[CEU][hapmap]
rs7298440	0.85[CEU][hapmap]
rs7298831	0.88[CEU][hapmap]
rs7302183	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302649	0.85[CEU][hapmap]
rs7306549	0.89[CEU][hapmap]
rs7307008	0.88[CEU][hapmap]
rs7307343	0.85[CEU][hapmap]
rs7308234	0.82[CEU][hapmap]
rs7308862	0.89[CEU][hapmap]
rs7309528	0.85[CEU][hapmap]
rs7310918	0.85[CEU][hapmap]
rs7313032	0.89[CEU][hapmap]
rs7313261	0.89[CEU][hapmap]
rs7313628	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7399224	0.85[CEU][hapmap]
rs786422	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786423	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786425	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786441	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs786443	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786444	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786445	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786447	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786449	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786452	0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs786454	0.81[AFR][1000 genomes]
rs7953599	0.85[CEU][hapmap]
rs7958693	0.92[CEU][hapmap]
rs7959553	0.84[CEU][hapmap]
rs7963968	0.85[CEU][hapmap]
rs7964443	0.89[CEU][hapmap]
rs7966867	0.92[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs7966882	0.81[EUR][1000 genomes]
rs7972413	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973155	0.84[CEU][hapmap]
rs7973695	0.84[CEU][hapmap]
rs7974279	0.89[CEU][hapmap]
rs7975119	0.85[CEU][hapmap]
rs7975233	0.85[CEU][hapmap]
rs7978447	0.85[CEU][hapmap]
rs7979528	0.85[CEU][hapmap]
rs884892	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs908373	0.92[CEU][hapmap];0.81[ASN][1000 genomes]
rs9919	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4456350	DDX55	cis	cerebellum	SCAN
rs4456350	DDX55	cis	parietal	SCAN
rs4456350	SETD1B	cis	parietal	SCAN
rs4456350	TCTN2	cis	cerebellum	SCAN
rs4456350	CABP1	cis	cerebellum	SCAN
rs4456350	ABCB9	cis	parietal	SCAN
rs4456350	TCTN2	cis	parietal	SCAN
rs4456350	TCTN2	cis	Adipose Subcutaneous	GTEx
rs4456350	TCTN2	cis	Artery Tibial	GTEx
rs4456350	DDX55	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124055000-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:124055000-124067400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr12:124055200-124060800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124055200-124068000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:124055400-124067800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:124055800-124060400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:124055800-124060600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:124056000-124060800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:124056000-124066600	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:124056000-124066600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr12:124056000-124067000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:124056000-124067800	Weak transcription	Lung	lung
13	chr12:124056200-124060600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:124056200-124064800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:124056200-124065000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:124056200-124066600	Weak transcription	Thymus	Thymus
17	chr12:124056200-124067000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr12:124056200-124067200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:124056400-124060400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:124056400-124060400	Weak transcription	A549	lung
21	chr12:124056400-124060600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:124056400-124065200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:124056400-124065400	Weak transcription	Osteobl	bone
24	chr12:124056400-124066600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:124056400-124066600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:124056400-124066600	Weak transcription	Brain Anterior Caudate	brain
27	chr12:124056400-124066600	Weak transcription	K562	blood
28	chr12:124056400-124066800	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:124056400-124066800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:124056400-124067000	Weak transcription	NHDF-Ad	bronchial
31	chr12:124056400-124067400	Weak transcription	HSMMtube	muscle
32	chr12:124056800-124066600	Weak transcription	Dnd41	blood
33	chr12:124058000-124058600	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr12:124058400-124058600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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