Variant report

Variant	rs10747573
Chromosome Location	chr12:50633839-50633840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10783342	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2160994	0.81[CEU][hapmap]
rs2358538	0.85[GIH][hapmap]
rs4459386	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs7957659	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs7967954	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs8181679	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]

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	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
2	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
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10747573	DBN1	trans	lymphoblastoid	seeQTL
rs10747573	NELL2	cis	cerebellum	SCAN
rs10747573	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs10747573	SLC4A8	cis	parietal	SCAN
rs10747573	LASS5	cis	cerebellum	SCAN
rs10747573	TMEM106C	cis	cerebellum	SCAN
rs10747573	LASS5	cis	multi-tissue	Pritchard
rs10747573	MCRS1	cis	parietal	SCAN
rs10747573	DIP2B	cis	cerebellum	SCAN
rs10747573	LASS5	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
2	chr12:50616400-50634000	Weak transcription	Gastric	stomach
3	chr12:50616400-50634000	Weak transcription	Ovary	ovary
4	chr12:50616400-50636200	Weak transcription	Left Ventricle	heart
5	chr12:50616600-50634000	Weak transcription	Colonic Mucosa	Colon
6	chr12:50616600-50634000	Weak transcription	Psoas Muscle	Psoas
7	chr12:50616600-50634000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:50616800-50636400	Weak transcription	Aorta	Aorta
9	chr12:50616800-50641600	Weak transcription	Brain Angular Gyrus	brain
10	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:50617000-50634000	Weak transcription	NHLF	lung
12	chr12:50617000-50636200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:50617400-50634600	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:50617400-50635600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:50617600-50638400	Weak transcription	Brain Germinal Matrix	brain
16	chr12:50618600-50634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:50618600-50634000	Weak transcription	Osteobl	bone
18	chr12:50618600-50634400	Weak transcription	HSMM	muscle
19	chr12:50618600-50636200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:50618600-50638400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:50618600-50640000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:50623000-50638400	Weak transcription	Fetal Brain Female	brain
23	chr12:50625400-50634000	Weak transcription	HSMMtube	muscle
24	chr12:50625400-50634400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:50627200-50635200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:50627400-50634000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:50627600-50634400	Weak transcription	Fetal Lung	lung
28	chr12:50627600-50644600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr12:50628400-50634000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:50628600-50634000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:50628600-50634000	Weak transcription	Spleen	Spleen
32	chr12:50628600-50634000	Weak transcription	A549	lung
33	chr12:50628800-50634000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:50628800-50634600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:50628800-50635200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:50628800-50640800	Weak transcription	Esophagus	oesophagus
37	chr12:50629000-50634000	Weak transcription	Hela-S3	cervix
38	chr12:50629000-50636000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:50629600-50634000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:50631400-50634200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:50631400-50638200	Weak transcription	Fetal Stomach	stomach
42	chr12:50631400-50638400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:50631800-50634000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:50632800-50634000	Enhancers	Adipose Nuclei	Adipose
45	chr12:50632800-50634000	Enhancers	Stomach Mucosa	stomach
46	chr12:50632800-50634200	Enhancers	K562	blood
47	chr12:50633000-50634200	Genic enhancers	Fetal Intestine Small	intestine
48	chr12:50633000-50634600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr12:50633000-50634800	Genic enhancers	Fetal Intestine Large	intestine
50	chr12:50633200-50634200	Enhancers	Lung	lung

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