Variant report

Variant	rs1781708
Chromosome Location	chr6:38604754-38604755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10807196	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs10807198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10947752	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1321056	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1699001	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699002	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1699003	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699004	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1699005	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1699007	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1699017	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1739621	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1739626	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1739627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1739628	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1739629	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1739630	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1739632	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1781711	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1781712	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1781738	0.85[EUR][1000 genomes]
rs1852979	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2144328	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2252550	0.92[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2748172	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2814883	0.92[CEU][hapmap];0.93[TSI][hapmap]
rs2814889	0.92[CEU][hapmap];0.90[TSI][hapmap]
rs2814894	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4392718	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs6458059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs910516	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394521	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1781708	BYSL	cis	cerebellum	SCAN
rs1781708	DNAH8	cis	cerebellum	SCAN
rs1781708	GLO1	cis	cerebellum	SCAN
rs1781708	GLO1	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38599600-38606200	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr6:38599600-38606600	Weak transcription	Lung	lung
3	chr6:38600600-38605600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:38600600-38606600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:38600800-38606600	Weak transcription	Right Ventricle	heart
6	chr6:38601000-38606400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:38601200-38607000	Weak transcription	Gastric	stomach
8	chr6:38601600-38606600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:38601800-38605000	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:38602000-38606600	Weak transcription	Psoas Muscle	Psoas
11	chr6:38602200-38605400	Weak transcription	Brain Anterior Caudate	brain
12	chr6:38602200-38606000	Weak transcription	Brain Germinal Matrix	brain
13	chr6:38602200-38606200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:38602200-38606400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr6:38602200-38606600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:38602400-38606000	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:38602400-38606000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:38602400-38606200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:38602400-38606600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:38602600-38606200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:38602600-38606200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr6:38602600-38606400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:38602600-38606400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:38602600-38606600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:38602800-38605400	Weak transcription	Fetal Heart	heart
26	chr6:38602800-38606200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr6:38602800-38606200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:38602800-38606400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:38602800-38606400	Weak transcription	Brain Substantia Nigra	brain
30	chr6:38602800-38606400	Weak transcription	HSMM	muscle
31	chr6:38602800-38606600	Weak transcription	NH-A	brain
32	chr6:38603000-38605400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:38603000-38606400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:38603000-38606400	Weak transcription	HUVEC	blood vessel
35	chr6:38603000-38606600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:38603200-38605000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr6:38603400-38605800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:38603400-38606400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:38603400-38606600	Weak transcription	Left Ventricle	heart
40	chr6:38603600-38605200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr6:38603800-38604800	Enhancers	Liver	Liver
42	chr6:38603800-38606600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:38603800-38606600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:38604000-38604800	Enhancers	Primary T cells from cord blood	blood
45	chr6:38604000-38604800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr6:38604000-38604800	Enhancers	Fetal Intestine Large	intestine
47	chr6:38604200-38606200	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:38604200-38606600	Weak transcription	Thymus	Thymus
49	chr6:38604200-38606800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:38604400-38605200	Enhancers	Primary T cells fromperipheralblood	blood

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