Variant report

Variant	rs461887
Chromosome Location	chr6:33360787-33360788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr6:33358308-33361074	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:33358794-33361177	PFSK-1	brain:	n/a	n/a
3	MXI1	chr6:33358639-33361468	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr6:33358441-33361393	IMR90	lung:	n/a	n/a
5	RCOR1	chr6:33358571-33360804	K562	blood:	n/a	n/a
6	NR2F2	chr6:33358512-33361007	K562	blood:	n/a	n/a
7	MXI1	chr6:33358628-33361214	K562	blood:	n/a	n/a
8	POLR2A	chr6:33358889-33361243	IMR90	lung:	n/a	n/a
9	MTA3	chr6:33358347-33360985	GM12878	blood:	n/a	n/a
10	E2F4	chr6:33358937-33360983	MCF10A-Er-Src	breast:	n/a	n/a
11	HCFC1	chr6:33358279-33360947	Hela-S3	cervix:	n/a	n/a

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:32936666..32939842-chr6:33360330..33364086,3	MCF-7	breast:
2	chr6:33279554..33283546-chr6:33360483..33362156,3	MCF-7	breast:
3	chr6:32936394..32938328-chr6:33359727..33361307,2	K562	blood:
4	chr6:33356382..33361019-chr6:33384058..33388661,8	K562	blood:
5	chr6:33242419..33244049-chr6:33358539..33360870,2	MCF-7	breast:
6	chr6:33283316..33288344-chr6:33357863..33362367,8	K562	blood:
7	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
8	chr6:33239039..33242495-chr6:33357243..33362134,5	MCF-7	breast:
9	chr6:33264068..33267385-chr6:33357975..33361447,5	MCF-7	breast:
10	chr6:33359751..33362577-chr6:33420507..33423497,2	K562	blood:
11	chr6:33358575..33362850-chr6:33383674..33386989,4	MCF-7	breast:
12	chr6:33358270..33361160-chr6:33397889..33401606,4	K562	blood:
13	chr6:33357351..33361150-chr6:33373102..33380127,12	MCF-7	breast:
14	chr6:33285348..33292496-chr6:33357328..33361566,13	K562	blood:
15	chr6:33238428..33241280-chr6:33357854..33362793,6	MCF-7	breast:
16	chr6:33360629..33362485-chr6:33371591..33374109,2	MCF-7	breast:
17	chr6:33241732..33243308-chr6:33359602..33361155,2	K562	blood:
18	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
19	chr6:33280908..33284579-chr6:33359142..33361187,5	K562	blood:
20	chr6:33264179..33271329-chr6:33356528..33360865,9	K562	blood:
21	chr6:33256540..33259907-chr6:33358017..33361464,3	MCF-7	breast:
22	chr6:33283943..33291558-chr6:33357867..33362243,10	MCF-7	breast:
23	chr6:33243392..33248315-chr6:33357393..33361975,11	K562	blood:
24	chr6:33280708..33283139-chr6:33358214..33362149,5	K562	blood:
25	chr6:33358950..33361251-chr6:33421997..33423819,3	K562	blood:
26	chr6:33253660..33257073-chr6:33358023..33361324,4	K562	blood:
27	chr6:33356271..33363521-chr6:33371085..33380351,32	K562	blood:
28	chr6:33357884..33361160-chr6:33397889..33401606,5	K562	blood:
29	chr6:33283728..33287391-chr6:33357794..33361686,6	MCF-7	breast:
30	chr6:33265384..33269852-chr6:33356528..33361842,9	K562	blood:

No data

Variant related genes	Relation type
RPL35AP4	TF binding region
ENSG00000204256	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000237441	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11757273	0.84[ASN][1000 genomes]
rs12204193	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1613451	0.87[ASN][1000 genomes]
rs1755047	0.87[ASN][1000 genomes]
rs2274730	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2480487	0.86[ASN][1000 genomes]
rs2743	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2772373	0.89[ASN][1000 genomes]
rs2772387	0.84[ASN][1000 genomes]
rs2772390	0.86[ASN][1000 genomes]
rs2772392	0.85[ASN][1000 genomes]
rs3117320	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130001	0.83[EUR][1000 genomes]
rs3130002	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130006	0.82[AMR][1000 genomes]
rs3130007	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130015	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3130025	0.86[ASN][1000 genomes]
rs3130274	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130275	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130276	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs371005	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs391500	0.89[AMR][1000 genomes]
rs420714	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs442745	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs456993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs459927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461964	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4620113	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs465223	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs465474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs465506	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs465877	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467065	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66840884	0.83[ASN][1000 genomes]
rs6942045	0.88[AMR][1000 genomes]
rs9278025	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9278029	0.87[AMR][1000 genomes]
rs9357159	0.83[ASN][1000 genomes]
rs9368760	0.85[AMR][1000 genomes]
rs9380355	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380365	0.81[CHB][hapmap]
rs9461856	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33358600-33361000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:33358800-33360800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:33358800-33360800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:33358800-33360800	Active TSS	NHLF	lung
5	chr6:33358800-33361000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:33358800-33361000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:33358800-33361400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:33358800-33361800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:33359000-33360800	Active TSS	Colon Smooth Muscle	Colon
10	chr6:33359000-33361000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:33359000-33361200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:33359000-33361200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:33359000-33361200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:33359000-33362000	Active TSS	HSMM	muscle
15	chr6:33359000-33362600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:33359200-33360800	Active TSS	GM12878-XiMat	blood
17	chr6:33359200-33361000	Active TSS	Fetal Intestine Large	intestine
18	chr6:33359200-33361200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:33359400-33361200	Enhancers	Spleen	Spleen
20	chr6:33359600-33360800	Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:33359600-33360800	Bivalent/Poised TSS	HepG2	liver
22	chr6:33359600-33360800	Active TSS	NHDF-Ad	bronchial
23	chr6:33359600-33361000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:33359600-33361000	Active TSS	A549	lung
25	chr6:33359600-33361200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr6:33359600-33361200	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr6:33359800-33360800	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr6:33359800-33360800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr6:33359800-33360800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:33359800-33360800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr6:33359800-33360800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr6:33359800-33360800	Enhancers	Stomach Mucosa	stomach
33	chr6:33359800-33361000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr6:33359800-33361200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:33359800-33361200	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr6:33359800-33363400	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr6:33360000-33360800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr6:33360000-33360800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:33360000-33360800	Flanking Active TSS	Fetal Lung	lung
40	chr6:33360000-33361000	Flanking Active TSS	Fetal Intestine Small	intestine
41	chr6:33360000-33361200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:33360000-33361200	Active TSS	Fetal Muscle Trunk	muscle
43	chr6:33360000-33361200	Flanking Active TSS	Fetal Stomach	stomach
44	chr6:33360000-33361200	Flanking Active TSS	NH-A	brain
45	chr6:33360000-33361200	Flanking Active TSS	Osteobl	bone
46	chr6:33360000-33361400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr6:33360000-33361400	Flanking Active TSS	Fetal Thymus	thymus
48	chr6:33360000-33371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:33360000-33377400	Weak transcription	Small Intestine	intestine
50	chr6:33360000-33377600	Weak transcription	Right Atrium	heart

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