Variant report

Variant	rs13198938
Chromosome Location	chr6:56598426-56598427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 162 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10498811	0.83[EUR][1000 genomes]
rs10498812	0.81[CEU][hapmap]
rs10498813	0.81[CEU][hapmap]
rs11756551	0.83[AMR][1000 genomes]
rs11961141	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11961342	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11968575	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11970648	0.81[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs13191164	0.83[EUR][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192567	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13194625	0.81[CEU][hapmap]
rs13194904	0.81[CEU][hapmap]
rs13196211	0.82[EUR][1000 genomes]
rs13198204	0.83[AMR][1000 genomes]
rs13198399	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13200166	0.81[CEU][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs13200559	0.83[AMR][1000 genomes]
rs13200868	0.83[AMR][1000 genomes]
rs13201639	0.83[AMR][1000 genomes]
rs13201733	0.83[AMR][1000 genomes]
rs13203000	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13203681	0.81[CEU][hapmap]
rs13204466	0.81[CEU][hapmap]
rs13205013	0.83[EUR][1000 genomes]
rs13205667	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs13206849	0.83[EUR][1000 genomes]
rs13207768	0.81[CEU][hapmap];0.89[MEX][hapmap]
rs13208409	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13210876	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13213878	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13217390	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13218913	0.81[CEU][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]
rs13219546	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13219942	0.98[EUR][1000 genomes]
rs13220618	0.81[CEU][hapmap]
rs13220628	0.86[CEU][hapmap]
rs13220851	0.83[AMR][1000 genomes]
rs16888118	0.83[EUR][1000 genomes]
rs16888124	0.83[EUR][1000 genomes]
rs16888126	0.81[EUR][1000 genomes]
rs16888128	0.85[EUR][1000 genomes]
rs16888130	0.85[EUR][1000 genomes]
rs16888133	0.83[EUR][1000 genomes]
rs16888135	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16888171	0.81[CEU][hapmap]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.85[EUR][1000 genomes]
rs17684571	0.85[EUR][1000 genomes]
rs17684730	0.83[AMR][1000 genomes]
rs17684748	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs17684772	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs17684784	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs17684802	0.81[CEU][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]
rs17684878	0.81[CEU][hapmap]
rs17684884	0.81[CEU][hapmap]
rs17751682	0.85[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs17751695	1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs17751966	0.83[AMR][1000 genomes]
rs17751977	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs17752002	0.83[AMR][1000 genomes]
rs17752046	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs17752106	0.81[CEU][hapmap]
rs2967960	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2967963	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002003	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002004	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002006	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002007	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3002008	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002009	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3002010	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs3002011	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34171958	0.83[AMR][1000 genomes]
rs34228698	0.83[AMR][1000 genomes]
rs34429594	0.97[EUR][1000 genomes]
rs34455199	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34463732	0.91[EUR][1000 genomes]
rs34465210	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34500949	0.83[AMR][1000 genomes]
rs34566275	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34576803	0.82[EUR][1000 genomes]
rs34587484	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34623351	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34640766	0.83[AMR][1000 genomes]
rs34703847	0.93[EUR][1000 genomes]
rs34724718	0.83[EUR][1000 genomes]
rs34803237	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34812826	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34824960	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34832779	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35089136	0.81[EUR][1000 genomes]
rs35206656	0.85[EUR][1000 genomes]
rs35251663	0.83[AMR][1000 genomes]
rs35326806	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35408048	0.83[EUR][1000 genomes]
rs35440822	0.83[AMR][1000 genomes]
rs35494794	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35566812	0.83[AMR][1000 genomes]
rs35619924	0.83[EUR][1000 genomes]
rs35637749	0.83[EUR][1000 genomes]
rs35668437	0.83[EUR][1000 genomes]
rs35687635	0.85[EUR][1000 genomes]
rs35876418	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35920751	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35986172	0.87[AMR][1000 genomes]
rs36022925	0.81[AMR][1000 genomes]
rs36068365	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4072271	0.85[EUR][1000 genomes]
rs4074101	0.85[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4074102	0.83[EUR][1000 genomes]
rs4074103	0.81[EUR][1000 genomes]
rs41267675	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4275049	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4299824	0.81[CEU][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes]
rs4348308	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs4371846	0.81[CEU][hapmap];0.83[AMR][1000 genomes]
rs4415160	0.81[CEU][hapmap];0.89[MEX][hapmap]
rs4457154	0.81[CEU][hapmap]
rs4640889	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.83[EUR][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs56368885	0.81[AMR][1000 genomes]
rs59085778	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59247267	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59432342	0.81[AMR][1000 genomes]
rs60498201	0.99[EUR][1000 genomes]
rs62411366	0.83[AMR][1000 genomes]
rs62411367	0.83[AMR][1000 genomes]
rs62411375	0.81[AMR][1000 genomes]
rs62412526	0.83[EUR][1000 genomes]
rs62412528	0.83[EUR][1000 genomes]
rs62412531	0.83[EUR][1000 genomes]
rs62412532	0.83[EUR][1000 genomes]
rs62412544	0.92[EUR][1000 genomes]
rs62412556	0.99[EUR][1000 genomes]
rs6901176	0.83[EUR][1000 genomes]
rs6905603	0.81[CEU][hapmap]
rs6918949	0.81[CEU][hapmap]
rs6924375	0.83[EUR][1000 genomes]
rs6926134	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6928104	0.83[AMR][1000 genomes]
rs6934714	0.81[CEU][hapmap]
rs6938003	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564848	0.82[EUR][1000 genomes]
rs71564849	0.85[EUR][1000 genomes]
rs71564855	0.83[AMR][1000 genomes]
rs71564856	0.83[AMR][1000 genomes]
rs71564861	0.83[AMR][1000 genomes]
rs7758867	0.81[CEU][hapmap]
rs7761501	0.81[CEU][hapmap];0.89[MEX][hapmap]
rs7761729	0.81[CEU][hapmap]
rs7767128	0.83[EUR][1000 genomes]
rs7771085	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13198938	BMP5	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56582600-56611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:56584800-56599800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:56588800-56603400	Weak transcription	Right Ventricle	heart
4	chr6:56590200-56607000	Weak transcription	Pancreas	Pancrea
5	chr6:56590400-56602200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:56590400-56604800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:56590600-56602200	Weak transcription	Brain Hippocampus Middle	brain
8	chr6:56590600-56605200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:56592200-56599200	Enhancers	NHLF	lung
10	chr6:56592200-56599400	Genic enhancers	HSMM	muscle
11	chr6:56592600-56603400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr6:56592800-56603600	Weak transcription	Right Atrium	heart
13	chr6:56592800-56605000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:56592800-56606000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:56592800-56606800	Weak transcription	Aorta	Aorta
16	chr6:56592800-56611800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:56593400-56604800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:56593400-56605200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:56593400-56605400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:56593400-56606800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:56593600-56605000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:56594800-56605000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr6:56594800-56607000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:56595000-56599800	Enhancers	Colon Smooth Muscle	Colon
26	chr6:56595200-56605000	Weak transcription	Fetal Intestine Small	intestine
27	chr6:56595400-56599000	Enhancers	Rectal Smooth Muscle	rectum
28	chr6:56596000-56599000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:56596000-56604400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:56596000-56605000	Weak transcription	Adipose Nuclei	Adipose
31	chr6:56596200-56599200	Weak transcription	GM12878-XiMat	blood
32	chr6:56596200-56600800	Weak transcription	Left Ventricle	heart
33	chr6:56596400-56606200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:56596400-56606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:56596400-56606800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:56597000-56598600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:56597400-56599800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:56597400-56606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:56597600-56598800	Weak transcription	Brain Substantia Nigra	brain
40	chr6:56597600-56599400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:56597800-56598800	Weak transcription	Fetal Heart	heart
42	chr6:56597800-56599200	Genic enhancers	Liver	Liver
43	chr6:56597800-56599400	Enhancers	A549	lung
44	chr6:56597800-56604800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr6:56597800-56605000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:56597800-56606000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:56598000-56598600	Strong transcription	HSMMtube	muscle
48	chr6:56598000-56599000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:56598000-56599200	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:56598000-56599400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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