Variant report

Variant	rs302984
Chromosome Location	chr6:25113005-25113006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:25112619-25113023	MCF10A-Er-Src	breast:	n/a	chr6:25112795-25112806 chr6:25112692-25112701
2	EP300	chr6:25112528-25113005	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:25112931-25113085	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr6:25112458-25113123	Hela-S3	cervix:	n/a	n/a
5	MYC	chr6:25112417-25113115	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr6:25112171-25113249	Hela-S3	cervix:	n/a	chr6:25112734-25112746 chr6:25112253-25112264
7	TCF7L2	chr6:25112769-25113091	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr6:25112585-25113023	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25112288..25113816-chr6:25114376..25117367,2	MCF-7	breast:
2	chr6:25111673..25113955-chr6:25164740..25166276,2	MCF-7	breast:
3	chr6:25110856..25114923-chr6:25121965..25124614,3	MCF-7	breast:

Variant related genes	Relation type
CMAHP	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1547054	1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AMR][1000 genomes]
rs1547055	0.91[JPT][hapmap]
rs1823184	0.85[AFR][1000 genomes]
rs1923195	0.94[ASW][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2145769	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2295737	0.91[JPT][hapmap]
rs2516577	0.91[JPT][hapmap]
rs2894033	0.94[ASW][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs302967	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs302968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.86[EUR][1000 genomes]
rs302969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs302970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs302977	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs302978	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]
rs302979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs302983	0.83[CHD][hapmap]
rs302986	0.85[EUR][1000 genomes]
rs302989	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]
rs302990	0.82[CHD][hapmap];0.80[LWK][hapmap]
rs303016	0.84[CHD][hapmap]
rs303018	0.84[CHD][hapmap]
rs303022	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs303025	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812105	0.80[CHD][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3818267	0.88[ASW][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap]
rs3818270	0.88[ASW][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap]
rs4712887	0.81[CHD][hapmap];0.91[JPT][hapmap]
rs6919920	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs6935318	0.88[ASW][hapmap];0.81[LWK][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap]
rs7740661	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7740668	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7773802	0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7775959	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7776121	0.84[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9379721	0.85[AFR][1000 genomes]
rs9393613	1.00[JPT][hapmap]
rs9393615	0.82[AFR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs302984	CMAH	cis	parietal	SCAN
rs302984	CMAH	cis	cerebellum	SCAN
rs302984	HIST1H2AG	cis	parietal	SCAN
rs302984	BTN2A1	cis	cerebellum	SCAN
rs302984	CMAH	cis	lymphoblastoid	seeQTL
rs302984	LRRC16A	cis	parietal	SCAN
rs302984	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs302984	ZNF204P	cis	parietal	SCAN
rs302984	SOX4	cis	parietal	SCAN

Chromatin state (count:75 , 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	chr6:25101400-25115800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:25102000-25116200	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr6:25102800-25117600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:25103200-25116000	Strong transcription	Primary hematopoietic stem cells	blood
15	chr6:25103200-25116000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:25103400-25116000	Strong transcription	Primary T cells from cord blood	blood
17	chr6:25103600-25116000	Strong transcription	HSMMtube	muscle
18	chr6:25103800-25134800	Weak transcription	Psoas Muscle	Psoas
19	chr6:25104800-25136800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr6:25105200-25116000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr6:25105600-25115600	Weak transcription	Pancreas	Pancrea
22	chr6:25105600-25116000	Strong transcription	Placenta	Placenta
23	chr6:25105800-25115000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:25105800-25115000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:25106000-25115600	Weak transcription	Right Ventricle	heart
26	chr6:25106000-25119800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:25106400-25122200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr6:25107200-25122200	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:25108600-25113200	Weak transcription	Spleen	Spleen
30	chr6:25108600-25116000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr6:25108800-25113200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:25108800-25113600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:25108800-25113800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:25108800-25116400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:25108800-25122000	Weak transcription	Colonic Mucosa	Colon
36	chr6:25108800-25125800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:25109000-25113800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:25109000-25113800	Weak transcription	HSMM	muscle
39	chr6:25109600-25114600	Strong transcription	GM12878-XiMat	blood
40	chr6:25110200-25123600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:25110400-25122800	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:25110800-25113600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:25110800-25113600	Weak transcription	Left Ventricle	heart
44	chr6:25110800-25113800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr6:25110800-25114200	Weak transcription	Ovary	ovary
46	chr6:25110800-25133400	Weak transcription	Aorta	Aorta
47	chr6:25111000-25114600	Enhancers	Hela-S3	cervix
48	chr6:25111000-25116000	Strong transcription	Primary B cells from cord blood	blood
49	chr6:25111600-25113400	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr6:25111600-25114800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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