Variant report

Variant	rs7136648
Chromosome Location	chr12:50624822-50624823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10219559	0.91[AMR][1000 genomes]
rs1044370	0.81[ASW][hapmap]
rs10747573	0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs10783342	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783343	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1362984	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862042	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2004283	0.90[AMR][1000 genomes]
rs2160994	0.82[CHB][hapmap]
rs2358538	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs4459386	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768951	0.82[YRI][hapmap]
rs6580729	0.81[ASW][hapmap]
rs6580732	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580734	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580736	0.87[LWK][hapmap];0.82[YRI][hapmap]
rs7136570	0.89[ASW][hapmap];0.85[LWK][hapmap]
rs7279	0.89[ASW][hapmap];0.85[LWK][hapmap]
rs7297421	0.89[ASW][hapmap];0.85[LWK][hapmap]
rs7302981	0.89[ASW][hapmap];0.85[LWK][hapmap]
rs7308692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7532	0.89[ASW][hapmap]
rs7957659	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967954	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8181679	0.89[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668955	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7136648	EPLIN	cis	multi-tissue	Pritchard
rs7136648	FAM186B	cis	parietal	SCAN
rs7136648	KIAA1463	cis	multi-tissue	Pritchard
rs7136648	DIP2B	cis	cerebellum	SCAN
rs7136648	LASS5	cis	multi-tissue	Pritchard
rs7136648	LASS5	cis	cerebellum	SCAN
rs7136648	LASS5	cis	parietal	SCAN
rs7136648	SLC38A4	cis	parietal	SCAN
rs7136648	SLC4A8	cis	parietal	SCAN
rs7136648	CERS5	cis	Nerve Tibial	GTEx
rs7136648	MCRS1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
2	chr12:50609200-50633200	Weak transcription	Small Intestine	intestine
3	chr12:50616200-50633200	Weak transcription	Lung	lung
4	chr12:50616400-50628400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:50616400-50632000	Weak transcription	Fetal Brain Male	brain
6	chr12:50616400-50634000	Weak transcription	Gastric	stomach
7	chr12:50616400-50634000	Weak transcription	Ovary	ovary
8	chr12:50616400-50636200	Weak transcription	Left Ventricle	heart
9	chr12:50616600-50628200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr12:50616600-50632200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:50616600-50634000	Weak transcription	Colonic Mucosa	Colon
12	chr12:50616600-50634000	Weak transcription	Psoas Muscle	Psoas
13	chr12:50616600-50634000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:50616800-50625200	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50616800-50626800	Weak transcription	Fetal Kidney	kidney
16	chr12:50616800-50636400	Weak transcription	Aorta	Aorta
17	chr12:50616800-50641600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
19	chr12:50617000-50626800	Weak transcription	Adipose Nuclei	Adipose
20	chr12:50617000-50632800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:50617000-50634000	Weak transcription	NHLF	lung
22	chr12:50617000-50636200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:50617200-50628400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr12:50617200-50633000	Strong transcription	Fetal Intestine Small	intestine
25	chr12:50617400-50626800	Weak transcription	Fetal Lung	lung
26	chr12:50617400-50634600	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:50617400-50635600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:50617600-50638400	Weak transcription	Brain Germinal Matrix	brain
29	chr12:50618400-50625200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:50618600-50625000	Weak transcription	HSMMtube	muscle
31	chr12:50618600-50626800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:50618600-50627000	Weak transcription	Stomach Mucosa	stomach
33	chr12:50618600-50628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:50618600-50628400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:50618600-50628400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:50618600-50628400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:50618600-50633800	Weak transcription	NHDF-Ad	bronchial
38	chr12:50618600-50634000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:50618600-50634000	Weak transcription	Osteobl	bone
40	chr12:50618600-50634400	Weak transcription	HSMM	muscle
41	chr12:50618600-50636200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:50618600-50638400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:50618600-50640000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:50618800-50626200	Weak transcription	Hela-S3	cervix
45	chr12:50619000-50626600	Weak transcription	GM12878-XiMat	blood
46	chr12:50619000-50628000	Weak transcription	Placenta	Placenta
47	chr12:50619400-50625400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:50619400-50626200	Strong transcription	Fetal Intestine Large	intestine
49	chr12:50621400-50626200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr12:50622400-50626400	Weak transcription	Fetal Muscle Leg	muscle

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