Variant report

Variant	rs302973
Chromosome Location	chr6:25119270-25119271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1002596	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs159988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs167329	0.88[JPT][hapmap]
rs16890104	1.00[ASW][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2028973	0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap]
rs2166682	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2166683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs302966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs302976	0.88[JPT][hapmap]
rs302980	0.88[JPT][hapmap]
rs302983	0.91[CHD][hapmap];0.88[JPT][hapmap]
rs302987	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs302990	0.90[CHD][hapmap]
rs302991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303000	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs303004	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303006	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs303015	0.84[JPT][hapmap]
rs303016	0.88[JPT][hapmap]
rs303018	0.88[JPT][hapmap]
rs303026	0.88[JPT][hapmap]
rs3792970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3792971	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3792986	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3818268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs391626	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs392852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs398672	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs420369	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs456816	1.00[CHB][hapmap]
rs57304238	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57796643	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6906102	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs715426	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7740661	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs7740668	0.86[CHB][hapmap]
rs9295646	1.00[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs9295647	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9393613	0.86[CHB][hapmap]
rs9393617	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs302973	CMAH	cis	cerebellum	SCAN
rs302973	CMAH	cis	parietal	SCAN
rs302973	CMAH	cis	lymphoblastoid	seeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
2	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
3	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
4	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:25106400-25122200	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:25107200-25122200	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:25108800-25122000	Weak transcription	Colonic Mucosa	Colon
9	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:25110400-25122800	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
13	chr6:25113000-25136800	Weak transcription	Osteobl	bone
14	chr6:25113400-25124200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr6:25113600-25132800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:25113800-25121200	Genic enhancers	Dnd41	blood
17	chr6:25114000-25130600	Weak transcription	Fetal Lung	lung
18	chr6:25114200-25122200	Weak transcription	HSMM	muscle
19	chr6:25114600-25122200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:25114600-25125800	Weak transcription	GM12878-XiMat	blood
21	chr6:25114800-25121800	Weak transcription	Adipose Nuclei	Adipose
22	chr6:25114800-25122200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:25114800-25122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:25114800-25122400	Weak transcription	Ovary	ovary
25	chr6:25114800-25122400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:25114800-25123000	Weak transcription	Spleen	Spleen
27	chr6:25114800-25123200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:25114800-25123600	Weak transcription	Thymus	Thymus
29	chr6:25114800-25124800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:25114800-25125800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:25114800-25127800	Weak transcription	Left Ventricle	heart
32	chr6:25115000-25121800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:25115000-25122800	Weak transcription	Liver	Liver
34	chr6:25115200-25121600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:25115400-25121800	Weak transcription	HUVEC	blood vessel
36	chr6:25115800-25123600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:25115800-25124000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:25116000-25119800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:25116000-25122200	Weak transcription	Primary B cells from cord blood	blood
40	chr6:25116000-25122200	Weak transcription	Placenta	Placenta
41	chr6:25116000-25122400	Weak transcription	HSMMtube	muscle
42	chr6:25116000-25123000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:25116000-25123600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:25116000-25137000	Weak transcription	Lung	lung
45	chr6:25116200-25119600	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr6:25117400-25120800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:25117800-25120600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:25118000-25119600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:25118200-25120000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:25118200-25120600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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