Variant report

Variant	rs4712887
Chromosome Location	chr6:25099566-25099567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25083346..25086259-chr6:25098635..25100927,2	MCF-7	breast:
2	chr6:25096659..25099596-chr6:25104363..25107003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168405	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12197057	0.83[ASW][hapmap]
rs1547054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1547055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs159988	0.85[CHD][hapmap]
rs16890104	0.81[CHD][hapmap]
rs1823184	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1838967	0.80[ASN][1000 genomes]
rs1923195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2145769	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2166682	0.81[ASN][1000 genomes]
rs2295737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516577	0.95[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];0.87[ASN][1000 genomes]
rs2894033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs302967	0.91[JPT][hapmap]
rs302968	0.92[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302969	0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs302970	0.91[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs302977	0.88[ASN][1000 genomes]
rs302978	0.88[ASN][1000 genomes]
rs302979	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs302984	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs302986	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs302989	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]
rs303000	0.81[CHD][hapmap]
rs303006	0.85[CHD][hapmap]
rs303009	0.85[CHD][hapmap]
rs303015	1.00[YRI][hapmap]
rs303016	0.89[CHD][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs303018	0.89[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs303019	0.91[ASW][hapmap];0.80[MKK][hapmap]
rs303022	0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs303023	0.86[AMR][1000 genomes]
rs303025	0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3792970	0.82[ASN][1000 genomes]
rs3792971	0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs3812105	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392852	0.85[CHD][hapmap]
rs4711078	0.82[ASN][1000 genomes]
rs6919920	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740661	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740668	0.89[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7773802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775959	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7776121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295646	0.85[CHD][hapmap]
rs9295647	0.89[CHD][hapmap]
rs9379721	0.80[ASN][1000 genomes]
rs9393613	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393615	0.87[EUR][1000 genomes]
rs9393616	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9393617	0.85[CHD][hapmap];0.81[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4712887	CMAH	cis	lymphoblastoid	seeQTL
rs4712887	HIST1H2AG	cis	parietal	SCAN
rs4712887	CMAH	cis	cerebellum	SCAN
rs4712887	CMAH	cis	parietal	SCAN
rs4712887	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs4712887	SOX4	cis	parietal	SCAN
rs4712887	LRRC16A	cis	parietal	SCAN
rs4712887	CMAH	cis	normal skin	skin_eQTL
rs4712887	ZNF204P	cis	parietal	SCAN
rs4712887	CMAHP	cis	Thyroid	GTEx
rs4712887	BTN2A1	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:25084800-25113800	Weak transcription	Gastric	stomach
3	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
5	chr6:25087000-25105400	Weak transcription	GM12878-XiMat	blood
6	chr6:25087400-25101600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:25087400-25113800	Strong transcription	Fetal Thymus	thymus
8	chr6:25087600-25105400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:25087600-25124800	Weak transcription	Small Intestine	intestine
10	chr6:25088000-25105800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:25088400-25105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr6:25088400-25113800	Strong transcription	Dnd41	blood
13	chr6:25089200-25106000	Weak transcription	Osteobl	bone
14	chr6:25089200-25108400	Weak transcription	HSMM	muscle
15	chr6:25089800-25103600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:25090400-25103600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:25090400-25105400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr6:25091600-25103600	Weak transcription	HSMMtube	muscle
19	chr6:25091600-25116000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:25091800-25103600	Weak transcription	Psoas Muscle	Psoas
21	chr6:25091800-25127800	Weak transcription	Esophagus	oesophagus
22	chr6:25093400-25100600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:25093400-25106800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:25093600-25102800	Weak transcription	Left Ventricle	heart
25	chr6:25094200-25105800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:25095400-25106400	Weak transcription	Spleen	Spleen
27	chr6:25095600-25105600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:25095600-25107000	Weak transcription	Colonic Mucosa	Colon
29	chr6:25095800-25106400	Weak transcription	Primary B cells from cord blood	blood
30	chr6:25096000-25103400	Weak transcription	Primary T cells from cord blood	blood
31	chr6:25096000-25116000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:25096400-25102800	Weak transcription	Thymus	Thymus
33	chr6:25096400-25103400	Weak transcription	Aorta	Aorta
34	chr6:25096400-25105600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr6:25096400-25106000	Weak transcription	Ovary	ovary
36	chr6:25096400-25118200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:25096600-25099600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr6:25096600-25099600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:25096600-25103800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:25096600-25105600	Weak transcription	Adipose Nuclei	Adipose
41	chr6:25096800-25106200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:25097000-25103000	Weak transcription	Liver	Liver
43	chr6:25097000-25105800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:25097000-25106600	Weak transcription	Lung	lung
45	chr6:25097200-25103200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:25097200-25103600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:25097600-25102800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr6:25097600-25103400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:25098000-25103000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr6:25098600-25100400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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