Variant report

Variant	rs10783336
Chromosome Location	chr12:50543422-50543423
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50541938..50544688-chr12:50559536..50561321,3	MCF-7	breast:
2	chr12:50533908..50538982-chr12:50540914..50544444,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10735822	0.84[EUR][1000 genomes]
rs10735823	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747571	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783337	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10783339	0.89[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10783341	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10875999	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876001	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876002	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876004	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10876006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876007	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876011	0.80[ASN][1000 genomes]
rs11169283	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169285	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12229758	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12314572	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17124448	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1862044	0.89[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs2008537	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242507	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2277355	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3782323	0.81[GIH][hapmap]
rs55639096	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56151073	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7131794	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139363	0.81[GIH][hapmap]
rs7297864	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7300549	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7305558	0.81[GIH][hapmap]
rs7306213	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73106145	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73106156	0.85[ASN][1000 genomes]
rs7314598	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7316344	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7397849	0.85[ASN][1000 genomes]
rs7486874	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953174	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10783336	SMARCD1	cis	cerebellum	SCAN
rs10783336	MCRS1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
3	chr12:50529800-50559800	Weak transcription	NHLF	lung
4	chr12:50530000-50559600	Weak transcription	A549	lung
5	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
6	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
7	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:50531800-50544600	Weak transcription	Fetal Kidney	kidney
9	chr12:50531800-50554400	Weak transcription	K562	blood
10	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
11	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
12	chr12:50532000-50560200	Weak transcription	Gastric	stomach
13	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
14	chr12:50533200-50544800	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:50534600-50544800	Weak transcription	Ovary	ovary
19	chr12:50535000-50545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:50535200-50545000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
23	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:50536800-50545000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:50537000-50544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
29	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:50537400-50550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:50537800-50544600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:50537800-50545000	Weak transcription	HMEC	breast
37	chr12:50537800-50545200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:50537800-50545200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:50537800-50547400	Weak transcription	Primary T cells from cord blood	blood
40	chr12:50537800-50550400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:50537800-50551200	Weak transcription	HepG2	liver
42	chr12:50537800-50553600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:50537800-50554200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:50537800-50554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:50537800-50554800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:50537800-50555800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:50537800-50556000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:50537800-50558200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:50537800-50558400	Weak transcription	Placenta	Placenta
50	chr12:50537800-50559200	Weak transcription	GM12878-XiMat	blood

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