Variant report

Variant	rs35080938
Chromosome Location	chr6:56712790-56712791
allele	C/T
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	MEF2A	chr6:56712765-56713452	GM12878	blood:	n/a	chr6:56713106-56713127 chr6:56713216-56713224 chr6:56713106-56713127 chr6:56713110-56713121 chr6:56713111-56713120 chr6:56713106-56713127 chr6:56713108-56713122 chr6:56713109-56713120
2	CEBPB	chr6:56712790-56713422	GM12878	blood:	n/a	chr6:56713411-56713422 chr6:56713409-56713422
3	NFIC	chr6:56712773-56713425	GM12878	blood:	n/a	n/a
4	NFIC	chr6:56712745-56713503	GM12878	blood:	n/a	n/a
5	MEF2C	chr6:56712765-56713337	GM12878	blood:	n/a	chr6:56713106-56713127 chr6:56713216-56713224 chr6:56713106-56713127 chr6:56713110-56713121 chr6:56713111-56713120 chr6:56713106-56713127 chr6:56713108-56713122 chr6:56713109-56713120
6	ATF2	chr6:56712790-56713379	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56707257..56710686-chr6:56712186..56717279,8	MCF-7	breast:
2	chr6:56712383..56714858-chr6:56818668..56820431,2	K562	blood:
3	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000231441	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10498812	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10498813	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11756551	0.85[EUR][1000 genomes]
rs13190854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13192540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13192931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13194625	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13194904	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13198204	0.88[EUR][1000 genomes]
rs13198597	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13200166	0.88[EUR][1000 genomes]
rs13200559	0.83[EUR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13200868	0.81[EUR][1000 genomes]
rs13201639	0.88[EUR][1000 genomes]
rs13201733	0.88[EUR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13203681	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13204466	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13205667	0.83[EUR][1000 genomes]
rs13207768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13208409	0.80[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13214893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13215883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13218913	0.88[EUR][1000 genomes]
rs13220618	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13220628	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13220851	0.90[EUR][1000 genomes]
rs1610156	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16888171	0.88[EUR][1000 genomes]
rs16888184	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16888186	0.94[EUR][1000 genomes]
rs16888192	0.80[EUR][1000 genomes]
rs17684730	0.88[EUR][1000 genomes]
rs17684748	0.88[EUR][1000 genomes]
rs17684772	0.88[EUR][1000 genomes]
rs17684784	0.88[EUR][1000 genomes]
rs17684802	0.88[EUR][1000 genomes]
rs17684878	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684884	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17751966	0.88[EUR][1000 genomes]
rs17751977	0.88[EUR][1000 genomes]
rs17752002	0.88[EUR][1000 genomes]
rs17752046	0.88[EUR][1000 genomes]
rs17752106	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752213	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1903332	0.96[EUR][1000 genomes]
rs28360570	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34083827	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34171958	0.89[EUR][1000 genomes]
rs34228698	0.88[EUR][1000 genomes]
rs34359353	0.89[EUR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34500949	0.83[EUR][1000 genomes]
rs34520435	0.89[EUR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34614087	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34640766	0.88[EUR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34896026	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34966024	0.82[EUR][1000 genomes]
rs35073881	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35081015	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35242294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35251663	0.88[EUR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35440408	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35440822	0.89[EUR][1000 genomes]
rs35461301	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35566812	0.86[EUR][1000 genomes]
rs35609883	0.88[EUR][1000 genomes]
rs35642890	0.88[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35851452	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35873865	0.86[EUR][1000 genomes]
rs35886823	0.88[EUR][1000 genomes]
rs35986172	0.80[EUR][1000 genomes]
rs36022925	0.88[EUR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs36094082	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4299824	0.88[EUR][1000 genomes]
rs4348308	0.88[EUR][1000 genomes]
rs4371846	0.88[EUR][1000 genomes]
rs4415160	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4457154	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4532444	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4587171	0.86[EUR][1000 genomes]
rs56037312	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56368885	0.82[EUR][1000 genomes]
rs58980183	0.82[EUR][1000 genomes]
rs59432342	0.88[EUR][1000 genomes]
rs61601344	0.88[EUR][1000 genomes]
rs62411366	0.81[EUR][1000 genomes]
rs62411367	0.83[EUR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62411375	0.88[EUR][1000 genomes]
rs62411376	0.88[EUR][1000 genomes]
rs6904535	0.83[EUR][1000 genomes]
rs6905603	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6910414	0.95[EUR][1000 genomes]
rs6914293	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6918949	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6928104	0.81[EUR][1000 genomes]
rs6934714	0.91[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs71564855	0.89[EUR][1000 genomes]
rs71564856	0.88[EUR][1000 genomes]
rs71564861	0.88[EUR][1000 genomes]
rs71564863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7758867	0.94[EUR][1000 genomes]
rs7761501	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7761729	0.99[EUR][1000 genomes]
rs7766565	0.94[EUR][1000 genomes]
rs7771085	0.94[EUR][1000 genomes]
rs7775182	0.90[AMR][1000 genomes];0.94[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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56709200-56714000	Weak transcription	Fetal Brain Male	brain
2	chr6:56709200-56714200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:56709200-56714400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:56709200-56714400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:56709200-56714400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:56709200-56714600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:56709200-56714600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:56709200-56714600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:56709200-56714600	Weak transcription	Psoas Muscle	Psoas
10	chr6:56709200-56715000	Weak transcription	Thymus	Thymus
11	chr6:56709200-56715400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:56709200-56715400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:56709200-56715400	Weak transcription	Aorta	Aorta
14	chr6:56709200-56716000	Weak transcription	Esophagus	oesophagus
15	chr6:56709400-56712800	Weak transcription	Osteobl	bone
16	chr6:56709400-56713000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:56709400-56714200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:56709400-56714200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:56709400-56714200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr6:56709400-56714200	Weak transcription	NH-A	brain
21	chr6:56709400-56714400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:56709400-56714400	Weak transcription	Fetal Brain Female	brain
23	chr6:56709400-56714400	Weak transcription	HSMM	muscle
24	chr6:56709400-56714400	Weak transcription	HUVEC	blood vessel
25	chr6:56709400-56714600	Weak transcription	Adipose Nuclei	Adipose
26	chr6:56709400-56714600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:56709400-56714800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:56709400-56714800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:56709400-56714800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:56709400-56714800	Weak transcription	HMEC	breast
31	chr6:56709400-56715400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr6:56709400-56716000	Weak transcription	Fetal Thymus	thymus
33	chr6:56709600-56715000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr6:56710000-56713000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:56710000-56714400	Weak transcription	HSMMtube	muscle
36	chr6:56710000-56714600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:56710000-56714600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:56710000-56715600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:56710200-56714800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:56710600-56714200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:56710800-56713400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr6:56710800-56714200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:56710800-56714200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:56710800-56714600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:56711000-56713600	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:56711000-56714200	Weak transcription	NHDF-Ad	bronchial
47	chr6:56711200-56714200	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:56711400-56714400	Weak transcription	A549	lung
49	chr6:56712200-56712800	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr6:56712200-56713000	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links