Variant report

Variant	rs302969
Chromosome Location	chr6:25128201-25128202
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1547054	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1547055	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1923195	0.91[JPT][hapmap]
rs2295737	0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2516577	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2894033	0.91[JPT][hapmap]
rs302967	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs302968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs302970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs302977	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302978	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]
rs302979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs302986	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs302989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs303015	1.00[YRI][hapmap]
rs303016	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs303018	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs303022	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303023	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs303025	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812105	0.91[JPT][hapmap]
rs4712887	0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs6919920	0.80[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7773802	0.91[JPT][hapmap]
rs7776121	0.84[JPT][hapmap]
rs9393613	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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
rs302969	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
2	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
4	chr6:25113000-25136800	Weak transcription	Osteobl	bone
5	chr6:25113600-25132800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:25114000-25130600	Weak transcription	Fetal Lung	lung
7	chr6:25116000-25137000	Weak transcription	Lung	lung
8	chr6:25120600-25129800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:25121000-25129800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:25122000-25131600	Strong transcription	Fetal Thymus	thymus
11	chr6:25122600-25132000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:25122600-25133800	Weak transcription	NHDF-Ad	bronchial
13	chr6:25122600-25137000	Weak transcription	Colonic Mucosa	Colon
14	chr6:25122600-25137000	Weak transcription	HSMM	muscle
15	chr6:25122800-25129400	Weak transcription	Ovary	ovary
16	chr6:25122800-25137000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:25123200-25130800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:25123600-25136600	Weak transcription	HSMMtube	muscle
19	chr6:25123800-25129400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:25123800-25136800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:25123800-25138400	Weak transcription	Pancreas	Pancrea
22	chr6:25124200-25129000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:25124400-25138200	Weak transcription	Spleen	Spleen
24	chr6:25125200-25128400	Weak transcription	Small Intestine	intestine
25	chr6:25125200-25130800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr6:25125400-25130000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr6:25125400-25130400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:25125400-25130400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:25126200-25130800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:25126200-25133000	Weak transcription	Primary B cells from cord blood	blood
31	chr6:25126200-25133200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:25126200-25136400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:25126400-25130800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr6:25126400-25131000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:25126400-25132000	Weak transcription	GM12878-XiMat	blood
36	chr6:25126400-25133200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr6:25126400-25133400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:25126400-25135400	Weak transcription	Thymus	Thymus
39	chr6:25126400-25136800	Weak transcription	Liver	Liver
40	chr6:25126800-25130800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:25127000-25129600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:25127400-25128600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr6:25127400-25129600	Strong transcription	Primary T cells from cord blood	blood
44	chr6:25127600-25128800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:25127800-25128400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:25127800-25128400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr6:25127800-25128400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:25127800-25128800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr6:25127800-25129000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr6:25127800-25129000	Strong transcription	Left Ventricle	heart

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