Variant report

Variant	rs302989
Chromosome Location	chr6:25108541-25108542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24719858..24721554-chr6:25106494..25110308,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12197057	0.83[ASW][hapmap]
rs1547054	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1547055	0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs159988	0.81[CHD][hapmap]
rs16890104	0.84[CHD][hapmap]
rs1923195	0.96[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2028973	0.81[CHD][hapmap]
rs2145769	0.90[ASN][1000 genomes]
rs2295737	0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2516577	0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2894033	0.96[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs302967	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs302968	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs302969	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]
rs302970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs302976	0.81[ASN][1000 genomes]
rs302977	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302978	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]
rs302979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302980	0.81[ASN][1000 genomes]
rs302983	0.87[MEX][hapmap]
rs302984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs302986	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303006	0.80[CHD][hapmap]
rs303009	0.81[CHD][hapmap]
rs303015	1.00[YRI][hapmap]
rs303016	0.92[CHD][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs303018	0.92[CHD][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs303019	0.91[ASW][hapmap];0.80[MKK][hapmap]
rs303022	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303023	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303025	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs303026	0.80[CHD][hapmap]
rs3792971	0.84[CHD][hapmap]
rs3812105	0.96[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs392852	0.81[CHD][hapmap]
rs4712887	1.00[ASW][hapmap];0.96[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6919920	0.88[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7740661	0.88[ASN][1000 genomes]
rs7740668	0.88[ASN][1000 genomes]
rs7773802	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7775959	0.85[ASN][1000 genomes]
rs7776121	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9295646	0.81[CHD][hapmap]
rs9295647	0.84[CHD][hapmap]
rs9393613	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9393616	0.89[ASN][1000 genomes]
rs9393617	0.81[CHD][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs302989	CMAH	cis	cerebellum	SCAN
rs302989	LRRC16A	cis	parietal	SCAN
rs302989	CMAH	cis	normal skin	skin_eQTL
rs302989	BTN2A1	cis	cerebellum	SCAN
rs302989	CMAH	cis	parietal	SCAN
rs302989	CMAH	cis	lymphoblastoid	seeQTL
rs302989	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs302989	SOX4	cis	parietal	SCAN
rs302989	HIST1H2AG	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25084800-25113800	Weak transcription	Gastric	stomach
2	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
3	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
4	chr6:25088400-25113800	Strong transcription	Dnd41	blood
5	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
7	chr6:25096000-25116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:25096400-25118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:25099000-25116200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:25099000-25117400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:25100800-25112200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:25101400-25115800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:25102000-25116200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr6:25102800-25110600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr6:25102800-25117600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:25103000-25110800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr6:25103000-25110800	Strong transcription	Liver	Liver
18	chr6:25103200-25116000	Strong transcription	Primary hematopoietic stem cells	blood
19	chr6:25103200-25116000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:25103400-25116000	Strong transcription	Primary T cells from cord blood	blood
21	chr6:25103600-25116000	Strong transcription	HSMMtube	muscle
22	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
23	chr6:25104200-25111000	Weak transcription	Brain Substantia Nigra	brain
24	chr6:25104600-25109400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr6:25105000-25112200	Weak transcription	Fetal Lung	lung
27	chr6:25105200-25109000	Strong transcription	Thymus	Thymus
28	chr6:25105200-25110600	Strong transcription	Stomach Smooth Muscle	stomach
29	chr6:25105200-25110800	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr6:25105200-25116000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:25105400-25110800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr6:25105400-25110800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:25105600-25109600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:25105600-25110400	Strong transcription	Adipose Nuclei	Adipose
35	chr6:25105600-25112400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:25105600-25115600	Weak transcription	Pancreas	Pancrea
37	chr6:25105600-25116000	Strong transcription	Placenta	Placenta
38	chr6:25105800-25115000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:25105800-25115000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:25106000-25109200	Strong transcription	Ovary	ovary
41	chr6:25106000-25110600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:25106000-25110800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:25106000-25115600	Weak transcription	Right Ventricle	heart
44	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
45	chr6:25106200-25110600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:25106400-25109000	Strong transcription	Primary B cells from cord blood	blood
47	chr6:25106400-25109000	Strong transcription	Osteobl	bone
48	chr6:25106400-25110800	Strong transcription	Aorta	Aorta
49	chr6:25106400-25110800	Strong transcription	Left Ventricle	heart
50	chr6:25106400-25112600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links