Variant report

Variant	rs10783337
Chromosome Location	chr12:50550543-50550544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50549438..50552015-chr12:50558255..50560974,3	K562	blood:
2	chr12:50482709..50484515-chr12:50550134..50551963,2	K562	blood:
3	chr12:50549433..50551816-chr12:50794598..50797488,2	K562	blood:
4	chr12:50482709..50485025-chr12:50550134..50552131,3	K562	blood:

Variant related genes	Relation type
ENSG00000161813	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10735823	0.81[EUR][1000 genomes]
rs10747571	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10783336	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	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783341	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10876001	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10876002	0.84[EUR][1000 genomes]
rs10876004	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10876006	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876007	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169283	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169284	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169285	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229758	0.81[EUR][1000 genomes]
rs12314572	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17124448	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1862044	0.89[CHB][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs2008537	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2242507	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2277355	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3782323	0.81[GIH][hapmap]
rs55639096	0.81[EUR][1000 genomes]
rs56151073	0.81[EUR][1000 genomes]
rs7131794	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7139363	0.81[GIH][hapmap]
rs7297864	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7300549	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7305558	0.81[GIH][hapmap]
rs7306213	0.85[EUR][1000 genomes]
rs73106145	0.86[EUR][1000 genomes]
rs7314598	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs7316344	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7486874	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[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
rs10783337	SMARCD1	cis	cerebellum	SCAN
rs10783337	MCRS1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
2	chr12:50529800-50559800	Weak transcription	NHLF	lung
3	chr12:50530000-50559600	Weak transcription	A549	lung
4	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
5	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:50531800-50554400	Weak transcription	K562	blood
7	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
8	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
9	chr12:50532000-50560200	Weak transcription	Gastric	stomach
10	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
11	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
16	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
20	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:50537400-50550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:50537800-50551200	Weak transcription	HepG2	liver
27	chr12:50537800-50553600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:50537800-50554200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr12:50537800-50554400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:50537800-50554800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr12:50537800-50555800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:50537800-50556000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:50537800-50558200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:50537800-50558400	Weak transcription	Placenta	Placenta
35	chr12:50537800-50559200	Weak transcription	GM12878-XiMat	blood
36	chr12:50537800-50559400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:50537800-50559400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:50537800-50559400	Weak transcription	Fetal Lung	lung
39	chr12:50537800-50559800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:50537800-50559800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:50537800-50560200	Weak transcription	Left Ventricle	heart
42	chr12:50538000-50554000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:50538000-50556000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr12:50538200-50550600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:50538200-50558200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:50538200-50559400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:50538200-50559800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr12:50538200-50559800	Weak transcription	Fetal Thymus	thymus
49	chr12:50538400-50550600	Weak transcription	NHDF-Ad	bronchial
50	chr12:50538400-50551600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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