Variant report

Variant	rs71564863
Chromosome Location	chr6:56705170-56705171
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr6:56704985-56709414	IMR90	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56689883..56694123-chr6:56703159..56705325,3	K562	blood:
2	chr6:56683662..56685940-chr6:56704272..56706946,2	MCF-7	breast:
3	chr6:56702437..56704205-chr6:56705017..56706715,2	MCF-7	breast:
4	chr6:56702761..56706423-chr6:56707121..56709805,6	MCF-7	breast:
5	chr6:56639761..56641864-chr6:56704493..56706002,2	MCF-7	breast:
6	chr6:56659782..56661301-chr6:56703853..56706024,2	MCF-7	breast:
7	chr6:56701741..56705807-chr6:56706748..56710604,7	MCF-7	breast:
8	chr6:56704167..56710132-chr6:56712428..56720773,11	MCF-7	breast:

No data

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

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10498812	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10498813	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11756551	0.85[EUR][1000 genomes]
rs13190854	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13192540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13194625	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13194904	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13198204	0.89[EUR][1000 genomes]
rs13198597	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13200166	0.89[EUR][1000 genomes]
rs13200559	0.84[EUR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13200868	0.82[EUR][1000 genomes]
rs13201639	0.89[EUR][1000 genomes]
rs13201733	0.89[EUR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13203681	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204466	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13205667	0.84[EUR][1000 genomes]
rs13207768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13208409	0.81[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13214893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13215883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13218913	0.89[EUR][1000 genomes]
rs13220618	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13220628	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13220851	0.91[EUR][1000 genomes]
rs1610156	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888171	0.89[EUR][1000 genomes]
rs16888184	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888186	0.93[EUR][1000 genomes]
rs17684730	0.89[EUR][1000 genomes]
rs17684748	0.89[EUR][1000 genomes]
rs17684772	0.89[EUR][1000 genomes]
rs17684784	0.89[EUR][1000 genomes]
rs17684802	0.89[EUR][1000 genomes]
rs17684878	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684884	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17751966	0.89[EUR][1000 genomes]
rs17751977	0.89[EUR][1000 genomes]
rs17752002	0.89[EUR][1000 genomes]
rs17752046	0.89[EUR][1000 genomes]
rs17752106	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752213	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1903332	0.95[EUR][1000 genomes]
rs28360570	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34083827	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34171958	0.90[EUR][1000 genomes]
rs34228698	0.89[EUR][1000 genomes]
rs34359353	0.90[EUR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34500949	0.84[EUR][1000 genomes]
rs34520435	0.90[EUR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34614087	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34640766	0.89[EUR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34896026	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34966024	0.83[EUR][1000 genomes]
rs35073881	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35080938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35081015	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35242294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35251663	0.88[EUR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35440408	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35440822	0.90[EUR][1000 genomes]
rs35461301	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35566812	0.87[EUR][1000 genomes]
rs35609883	0.89[EUR][1000 genomes]
rs35642890	0.89[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35851452	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35873865	0.87[EUR][1000 genomes]
rs35886823	0.89[EUR][1000 genomes]
rs35986172	0.81[EUR][1000 genomes]
rs36022925	0.89[EUR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs36094082	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4299824	0.89[EUR][1000 genomes]
rs4348308	0.89[EUR][1000 genomes]
rs4371846	0.89[EUR][1000 genomes]
rs4415160	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4457154	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4532444	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587171	0.86[EUR][1000 genomes]
rs56037312	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56368885	0.82[EUR][1000 genomes]
rs58980183	0.82[EUR][1000 genomes]
rs59432342	0.89[EUR][1000 genomes]
rs61601344	0.89[EUR][1000 genomes]
rs62411366	0.82[EUR][1000 genomes]
rs62411367	0.84[EUR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62411375	0.88[EUR][1000 genomes]
rs62411376	0.89[EUR][1000 genomes]
rs6904535	0.84[EUR][1000 genomes]
rs6905603	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6910414	0.94[EUR][1000 genomes]
rs6914293	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6918949	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6928104	0.82[EUR][1000 genomes]
rs6934714	0.93[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs71564855	0.90[EUR][1000 genomes]
rs71564856	0.89[EUR][1000 genomes]
rs71564861	0.89[EUR][1000 genomes]
rs7758867	0.96[EUR][1000 genomes]
rs7761501	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761729	0.98[EUR][1000 genomes]
rs7766565	0.93[EUR][1000 genomes]
rs7771085	0.94[EUR][1000 genomes]
rs7775182	0.90[AMR][1000 genomes];0.97[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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56684200-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:56693600-56705600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:56693800-56705400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:56694000-56705400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:56699600-56705600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:56699800-56705200	Weak transcription	Right Ventricle	heart
7	chr6:56700400-56705800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56701800-56705400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr6:56701800-56705400	Enhancers	Fetal Heart	heart
10	chr6:56702000-56705800	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:56702200-56705200	Enhancers	Brain Anterior Caudate	brain
12	chr6:56702200-56705400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:56702200-56705800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:56702400-56705400	Weak transcription	Fetal Muscle Leg	muscle
15	chr6:56702400-56705600	Weak transcription	Left Ventricle	heart
16	chr6:56702600-56705200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:56702600-56705400	Weak transcription	Ovary	ovary
18	chr6:56702600-56706600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:56703000-56705200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:56703000-56706000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:56703000-56707200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:56703200-56705200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:56703200-56705200	Enhancers	Brain Hippocampus Middle	brain
24	chr6:56703200-56705200	Enhancers	NHDF-Ad	bronchial
25	chr6:56703200-56705600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:56703200-56705600	Weak transcription	Hela-S3	cervix
27	chr6:56703600-56705600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:56703600-56705600	Enhancers	Colon Smooth Muscle	Colon
29	chr6:56703800-56705200	Enhancers	NHLF	lung
30	chr6:56703800-56705400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:56703800-56705400	Enhancers	HUVEC	blood vessel
32	chr6:56703800-56705600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:56703800-56705600	Enhancers	Fetal Brain Male	brain
34	chr6:56703800-56705800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr6:56703800-56706200	Enhancers	Rectal Smooth Muscle	rectum
36	chr6:56703800-56706400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr6:56704000-56705200	Enhancers	Osteobl	bone
38	chr6:56704000-56705400	Enhancers	Brain Germinal Matrix	brain
39	chr6:56704000-56705600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:56704000-56706400	Active TSS	Psoas Muscle	Psoas
41	chr6:56704000-56709400	Active TSS	Right Atrium	heart
42	chr6:56704200-56705200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:56704200-56705600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:56704200-56707400	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr6:56704200-56707600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr6:56704200-56709200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:56704400-56705200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:56704400-56705400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:56704600-56705600	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr6:56704600-56705800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links