Variant report

Variant	rs302978
Chromosome Location	chr6:25118110-25118111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1547054	0.82[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1547055	0.82[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs1923195	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2145769	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2295737	0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2516577	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs2894033	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs302967	0.94[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs302968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs302969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302976	0.81[ASN][1000 genomes]
rs302977	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302979	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302980	0.81[ASN][1000 genomes]
rs302984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs302986	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303022	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303023	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303025	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812105	0.80[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3818267	0.84[YRI][hapmap]
rs3818270	0.84[YRI][hapmap]
rs4712887	0.88[ASN][1000 genomes]
rs6919920	0.80[CHB][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs6935318	0.83[YRI][hapmap]
rs7740661	0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7740668	0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7773802	0.80[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7775959	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7776121	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9393613	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9393616	0.89[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs302978	CMAH	Cis_1M	lymphoblastoid	RTeQTL

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	chr6:25096400-25118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
5	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:25106400-25122200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:25107200-25122200	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:25108800-25122000	Weak transcription	Colonic Mucosa	Colon
10	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:25110400-25122800	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
14	chr6:25113000-25136800	Weak transcription	Osteobl	bone
15	chr6:25113400-25124200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:25113600-25132800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:25113800-25121200	Genic enhancers	Dnd41	blood
18	chr6:25114000-25130600	Weak transcription	Fetal Lung	lung
19	chr6:25114200-25122200	Weak transcription	HSMM	muscle
20	chr6:25114600-25122200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:25114600-25125800	Weak transcription	GM12878-XiMat	blood
22	chr6:25114800-25118200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:25114800-25118400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr6:25114800-25118600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:25114800-25121800	Weak transcription	Adipose Nuclei	Adipose
26	chr6:25114800-25122200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:25114800-25122200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr6:25114800-25122400	Weak transcription	Ovary	ovary
29	chr6:25114800-25122400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr6:25114800-25123000	Weak transcription	Spleen	Spleen
31	chr6:25114800-25123200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:25114800-25123600	Weak transcription	Thymus	Thymus
33	chr6:25114800-25124800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:25114800-25125800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:25114800-25127800	Weak transcription	Left Ventricle	heart
36	chr6:25115000-25118200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:25115000-25119200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr6:25115000-25121800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:25115000-25122800	Weak transcription	Liver	Liver
40	chr6:25115200-25121600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:25115400-25121800	Weak transcription	HUVEC	blood vessel
42	chr6:25115800-25118200	Weak transcription	Fetal Thymus	thymus
43	chr6:25115800-25123600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:25115800-25124000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:25116000-25118400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:25116000-25118400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:25116000-25118400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:25116000-25118600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:25116000-25118600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:25116000-25118800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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