Variant report

Variant	rs372205
Chromosome Location	chr6:149775267-149775268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11155639	0.80[TSI][hapmap]
rs11155641	1.00[ASW][hapmap];0.84[CEU][hapmap];0.91[TSI][hapmap];0.80[AFR][1000 genomes]
rs11155644	0.84[AFR][1000 genomes]
rs11964335	0.92[CEU][hapmap]
rs13219868	0.88[CEU][hapmap]
rs1446556	0.80[TSI][hapmap]
rs1900300	0.88[CEU][hapmap]
rs237003	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs237005	0.93[JPT][hapmap]
rs237009	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs237010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs237012	0.88[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs237016	0.88[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs237018	0.89[EUR][1000 genomes]
rs237019	0.83[EUR][1000 genomes]
rs237024	0.84[AFR][1000 genomes]
rs237025	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs237026	0.88[CEU][hapmap]
rs237028	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs237035	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs366905	0.90[EUR][1000 genomes]
rs372238	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs384334	0.84[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs394563	0.85[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs399673	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs409099	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs409111	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs412894	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs420099	0.93[ASN][1000 genomes]
rs420430	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421453	0.87[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs438852	0.85[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs444784	0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs447025	0.89[ASN][1000 genomes]
rs448420	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448874	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs480870	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895787	0.92[CEU][hapmap]
rs548848	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs584916	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6570963	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs6570964	0.88[CEU][hapmap]
rs6922130	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs6942381	0.96[CEU][hapmap]
rs805026	0.88[CEU][hapmap];0.86[EUR][1000 genomes]

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	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs372205	RAET1E	cis	cerebellum	SCAN
rs372205	SUMO4	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149768400-149779400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:149769600-149782800	Strong transcription	Primary B cells from peripheral blood	blood
3	chr6:149769600-149787200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:149769800-149779800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr6:149770000-149779600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:149770000-149785200	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr6:149771600-149778000	Weak transcription	GM12878-XiMat	blood
8	chr6:149771800-149775600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:149771800-149775800	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr6:149772000-149788800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:149772200-149776600	Enhancers	Liver	Liver
12	chr6:149772400-149776600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr6:149772400-149776600	Enhancers	Fetal Lung	lung
14	chr6:149772600-149776400	Enhancers	Small Intestine	intestine
15	chr6:149772600-149779400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:149772600-149787000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:149772800-149776400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr6:149773000-149776800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:149773000-149778200	Weak transcription	Thymus	Thymus
20	chr6:149773000-149779600	Weak transcription	Primary T cells from cord blood	blood
21	chr6:149773000-149783400	Strong transcription	Primary B cells from cord blood	blood
22	chr6:149773200-149776600	Enhancers	Colonic Mucosa	Colon
23	chr6:149773200-149776600	Enhancers	Duodenum Mucosa	Duodenum
24	chr6:149773400-149777000	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr6:149773600-149778400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:149774000-149775800	Enhancers	Fetal Muscle Trunk	muscle
27	chr6:149774000-149777000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:149774600-149776600	Enhancers	Fetal Muscle Leg	muscle
29	chr6:149774600-149776800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:149774600-149777000	Bivalent Enhancer	Fetal Stomach	stomach
31	chr6:149774800-149775400	Enhancers	Brain Hippocampus Middle	brain
32	chr6:149774800-149775400	Enhancers	Fetal Kidney	kidney
33	chr6:149774800-149775400	Enhancers	NHDF-Ad	bronchial
34	chr6:149774800-149775600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:149774800-149775600	Enhancers	HSMMtube	muscle
36	chr6:149774800-149775800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:149774800-149776000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr6:149774800-149776000	Enhancers	Aorta	Aorta
39	chr6:149774800-149776000	Enhancers	NHEK	skin
40	chr6:149774800-149776200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:149774800-149776200	Enhancers	Brain Germinal Matrix	brain
42	chr6:149774800-149776200	Enhancers	Fetal Intestine Large	intestine
43	chr6:149774800-149776200	Enhancers	Fetal Thymus	thymus
44	chr6:149774800-149776200	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr6:149774800-149776200	Enhancers	HSMM	muscle
46	chr6:149774800-149776400	Enhancers	Ovary	ovary
47	chr6:149774800-149776400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr6:149774800-149776600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:149774800-149776600	Flanking Active TSS	Hela-S3	cervix
50	chr6:149774800-149776800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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