Variant report

Variant	rs6918949
Chromosome Location	chr6:56709981-56709982
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	EP300	chr6:56709761-56710644	GM12878	blood:	n/a	n/a
2	ZNF384	chr6:56709808-56710331	GM12878	blood:	n/a	n/a
3	SIN3A	chr6:56709830-56710301	GM12878	blood:	n/a	n/a
4	STAT3	chr6:56709864-56710462	GM12878	blood:	n/a	n/a
5	BHLHE40	chr6:56709961-56710598	GM12878	blood:	n/a	n/a
6	EP300	chr6:56709942-56710148	GM12878	blood:	n/a	n/a
7	CHD2	chr6:56709944-56710266	GM12878	blood:	n/a	n/a
8	MXI1	chr6:56709926-56710133	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56707257..56710686-chr6:56712186..56717279,8	MCF-7	breast:
2	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs10498812	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10498813	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11756551	0.84[EUR][1000 genomes]
rs11968575	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs11970648	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs13190784	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs13190854	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13192540	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13192931	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13194625	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs13194904	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13195601	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13198204	0.88[EUR][1000 genomes]
rs13198597	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200166	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs13200559	0.82[EUR][1000 genomes]
rs13200768	0.86[EUR][1000 genomes]
rs13200868	0.80[EUR][1000 genomes]
rs13201639	0.88[EUR][1000 genomes]
rs13201733	0.88[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap]
rs13203148	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13203327	0.84[EUR][1000 genomes]
rs13203681	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13204466	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13207768	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13211879	0.93[EUR][1000 genomes]
rs13214893	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13215883	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13217390	0.81[CEU][hapmap]
rs13218913	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs13220618	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13220628	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs13220851	0.89[EUR][1000 genomes]
rs1610156	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1610157	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888171	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs16888184	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16888186	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888189	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs16888192	0.81[EUR][1000 genomes]
rs17684730	0.88[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17684784	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs17684802	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs17684878	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684884	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684941	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17751966	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17752002	0.88[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17752106	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752213	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1903332	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28360570	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002010	0.81[CEU][hapmap]
rs3002011	0.80[CEU][hapmap]
rs34083827	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34171958	0.88[EUR][1000 genomes]
rs34228698	0.88[EUR][1000 genomes]
rs34359353	0.88[EUR][1000 genomes]
rs34425815	0.87[EUR][1000 genomes]
rs34500949	0.82[EUR][1000 genomes]
rs34520435	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34612783	0.86[EUR][1000 genomes]
rs34614087	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34640766	0.88[EUR][1000 genomes]
rs34866877	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34896026	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34966024	0.81[EUR][1000 genomes]
rs35073881	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35080938	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35081015	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35225175	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35242294	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35251663	0.87[EUR][1000 genomes]
rs35407078	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35439100	0.95[EUR][1000 genomes]
rs35440408	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35440822	0.88[EUR][1000 genomes]
rs35461301	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35566812	0.85[EUR][1000 genomes]
rs35609883	0.88[EUR][1000 genomes]
rs35642890	0.88[EUR][1000 genomes]
rs35696739	0.88[EUR][1000 genomes]
rs35828379	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35851452	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35873865	0.85[EUR][1000 genomes]
rs35886823	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36022925	0.88[EUR][1000 genomes]
rs36037734	0.88[EUR][1000 genomes]
rs36094082	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4299824	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs4348308	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4371846	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4415160	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4457154	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4532444	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs56037312	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56368885	0.81[EUR][1000 genomes]
rs58980183	0.81[EUR][1000 genomes]
rs59432342	0.88[EUR][1000 genomes]
rs61601344	0.88[EUR][1000 genomes]
rs62411366	0.80[EUR][1000 genomes]
rs62411367	0.82[EUR][1000 genomes]
rs62411372	0.86[EUR][1000 genomes]
rs62411375	0.87[EUR][1000 genomes]
rs62411376	0.88[EUR][1000 genomes]
rs6904535	0.82[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6910414	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6914293	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6928104	0.80[EUR][1000 genomes]
rs6934714	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564854	0.88[EUR][1000 genomes]
rs71564855	0.88[EUR][1000 genomes]
rs71564856	0.88[EUR][1000 genomes]
rs71564861	0.88[EUR][1000 genomes]
rs71564863	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7758867	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7761501	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7761729	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7766565	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7771085	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7775182	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6918949	RAB23	cis	multi-tissue	Pritchard
rs6918949	BMP5	cis	cerebellum	SCAN
rs6918949	BEND6	cis	parietal	SCAN
rs6918949	DST	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56709000-56710000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:56709000-56710400	Weak transcription	NHDF-Ad	bronchial
3	chr6:56709200-56711000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr6:56709200-56711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56709200-56712200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:56709200-56712200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:56709200-56712200	Weak transcription	NHLF	lung
8	chr6:56709200-56712600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:56709200-56714000	Weak transcription	Fetal Brain Male	brain
10	chr6:56709200-56714200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:56709200-56714400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:56709200-56714400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:56709200-56714400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:56709200-56714600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:56709200-56714600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:56709200-56714600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:56709200-56714600	Weak transcription	Psoas Muscle	Psoas
18	chr6:56709200-56715000	Weak transcription	Thymus	Thymus
19	chr6:56709200-56715400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:56709200-56715400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:56709200-56715400	Weak transcription	Aorta	Aorta
22	chr6:56709200-56716000	Weak transcription	Esophagus	oesophagus
23	chr6:56709400-56710000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:56709400-56710000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr6:56709400-56710000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:56709400-56710000	Enhancers	Fetal Muscle Leg	muscle
27	chr6:56709400-56710000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr6:56709400-56710000	Enhancers	Stomach Smooth Muscle	stomach
29	chr6:56709400-56710000	Active TSS	HSMMtube	muscle
30	chr6:56709400-56710200	Weak transcription	Brain Germinal Matrix	brain
31	chr6:56709400-56710200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr6:56709400-56710200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:56709400-56710600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:56709400-56710600	Enhancers	Brain Substantia Nigra	brain
35	chr6:56709400-56710800	Enhancers	Brain Angular Gyrus	brain
36	chr6:56709400-56710800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr6:56709400-56711000	Enhancers	Brain Hippocampus Middle	brain
38	chr6:56709400-56711200	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr6:56709400-56711400	Enhancers	A549	lung
40	chr6:56709400-56712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr6:56709400-56712200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:56709400-56712400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:56709400-56712400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:56709400-56712800	Weak transcription	Osteobl	bone
45	chr6:56709400-56713000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:56709400-56714200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr6:56709400-56714200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:56709400-56714200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:56709400-56714200	Weak transcription	NH-A	brain
50	chr6:56709400-56714400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links