Variant report

Variant	rs12203399
Chromosome Location	chr6:71475355-71475356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10498874	0.85[MEX][hapmap]
rs10498876	0.81[MEX][hapmap]
rs10755541	0.85[MEX][hapmap]
rs10755543	0.81[MEX][hapmap]
rs1084388	0.85[MEX][hapmap]
rs10945243	0.85[MEX][hapmap]
rs10945246	0.81[MEX][hapmap]
rs10945247	0.81[MEX][hapmap]
rs12198750	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12202909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212629	0.85[MEX][hapmap]
rs12215757	0.85[MEX][hapmap]
rs12215835	0.81[MEX][hapmap]
rs13174	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1333966	1.00[ASW][hapmap]
rs1333967	0.81[MEX][hapmap]
rs1577108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1577110	0.85[MEX][hapmap]
rs1716007	0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs17763188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1855437	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347433	0.85[MEX][hapmap]
rs2460689	0.81[MEX][hapmap]
rs2474913	0.81[MEX][hapmap]
rs2474917	0.85[MEX][hapmap]
rs2504756	0.81[MEX][hapmap]
rs2504757	0.85[MEX][hapmap]
rs4613778	0.81[MEX][hapmap]
rs4706458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4706462	0.81[MEX][hapmap]
rs4706464	0.81[MEX][hapmap]
rs4707843	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707847	0.80[MEX][hapmap]
rs4707851	0.85[MEX][hapmap]
rs4707854	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4707855	0.81[MEX][hapmap]
rs615526	0.83[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7451673	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7760267	0.81[MEX][hapmap]
rs7771674	0.81[MEX][hapmap]
rs781967	0.85[MEX][hapmap]
rs781968	0.85[MEX][hapmap]
rs781969	0.81[MEX][hapmap]
rs781977	0.81[MEX][hapmap]
rs781978	0.81[MEX][hapmap]
rs781982	0.81[MEX][hapmap]
rs781983	0.81[MEX][hapmap]
rs781987	0.81[MEX][hapmap]
rs781989	0.85[MEX][hapmap]
rs781990	0.81[MEX][hapmap]
rs9364097	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9455215	0.81[MEX][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	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12203399	OGFRL1	cis	cerebellum	SCAN
rs12203399	FAM135A	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71428200-71476400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:71435800-71477600	Weak transcription	HSMM	muscle
3	chr6:71440400-71488800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:71443200-71488800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:71444800-71523600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:71445200-71482200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:71447800-71500600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:71451400-71483200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:71451800-71480200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr6:71451800-71481000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:71451800-71488200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:71451800-71488400	Weak transcription	Pancreas	Pancrea
13	chr6:71453000-71489800	Weak transcription	Psoas Muscle	Psoas
14	chr6:71460200-71480200	Weak transcription	Fetal Intestine Large	intestine
15	chr6:71461400-71481000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:71463200-71492600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:71463400-71488200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:71465800-71488200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr6:71466200-71476400	Weak transcription	Fetal Brain Female	brain
20	chr6:71466200-71485800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:71466200-71488400	Weak transcription	Aorta	Aorta
22	chr6:71466400-71476800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:71466400-71480200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:71466400-71481600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:71466400-71483400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:71466400-71487600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:71466400-71493200	Weak transcription	Dnd41	blood
28	chr6:71466400-71494800	Weak transcription	Small Intestine	intestine
29	chr6:71466400-71508800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr6:71466600-71482600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:71466600-71488600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:71467000-71486200	Weak transcription	Brain Germinal Matrix	brain
33	chr6:71468800-71532200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr6:71469200-71481200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:71469800-71488400	Weak transcription	Fetal Muscle Leg	muscle
36	chr6:71470000-71475800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr6:71471200-71481000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr6:71471200-71490600	Weak transcription	Right Ventricle	heart
39	chr6:71471800-71480800	Weak transcription	Lung	lung
40	chr6:71472000-71484800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:71472200-71488400	Weak transcription	Gastric	stomach
42	chr6:71472400-71488400	Weak transcription	Esophagus	oesophagus
43	chr6:71472600-71488400	Weak transcription	Spleen	Spleen
44	chr6:71473000-71515600	Weak transcription	Left Ventricle	heart
45	chr6:71473600-71475400	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr6:71473800-71481000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:71473800-71482200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:71473800-71488200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:71473800-71520200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:71474000-71482600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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