Variant report

Variant	rs6446553
Chromosome Location	chr4:6942857-6942858
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6908111..6910785-chr4:6941101..6945265,3	MCF-7	breast:
2	chr4:6911457..6914297-chr4:6942387..6944279,2	K562	blood:
3	chr4:6935997..6938458-chr4:6940561..6943507,2	K562	blood:
4	chr4:6942348..6944791-chr4:6958193..6960563,2	MCF-7	breast:
5	chr4:6940421..6944056-chr4:6949146..6952385,3	K562	blood:
6	chr4:6941935..6944212-chr4:6988372..6991479,3	K562	blood:
7	chr4:6941810..6943426-chr4:6944150..6946769,2	K562	blood:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10009332	0.88[ASN][1000 genomes]
rs10013211	1.00[JPT][hapmap]
rs10015163	1.00[JPT][hapmap]
rs10019900	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10804990	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10937762	0.95[JPT][hapmap]
rs10937763	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10937768	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10937769	0.87[ASN][1000 genomes]
rs10937770	0.98[ASN][1000 genomes]
rs10937771	0.88[ASN][1000 genomes]
rs11723651	0.98[ASN][1000 genomes]
rs11723686	0.88[ASN][1000 genomes]
rs11723719	0.98[ASN][1000 genomes]
rs11728984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11731639	0.98[ASN][1000 genomes]
rs11731681	0.87[ASN][1000 genomes]
rs11732389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11732887	0.92[ASN][1000 genomes]
rs11733522	0.92[ASN][1000 genomes]
rs11736355	0.98[ASN][1000 genomes]
rs11930747	0.94[ASN][1000 genomes]
rs11942739	0.85[ASN][1000 genomes]
rs12499678	0.98[ASN][1000 genomes]
rs13114976	0.85[ASN][1000 genomes]
rs13149280	0.95[ASN][1000 genomes]
rs13435015	0.85[JPT][hapmap]
rs17742611	0.86[JPT][hapmap]
rs2301820	0.86[JPT][hapmap]
rs28392702	0.87[ASN][1000 genomes]
rs28425595	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35490604	0.85[ASN][1000 genomes]
rs3857170	0.82[JPT][hapmap]
rs3892976	0.82[ASN][1000 genomes]
rs41516949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4234790	0.88[ASN][1000 genomes]
rs4261987	0.83[ASN][1000 genomes]
rs4315786	0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4346651	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4432749	0.86[JPT][hapmap]
rs4484301	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4513567	0.86[ASN][1000 genomes]
rs4608812	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4689055	0.87[ASN][1000 genomes]
rs4689057	0.90[ASN][1000 genomes]
rs4689558	0.95[JPT][hapmap]
rs4689562	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs58935653	0.84[ASN][1000 genomes]
rs61488923	0.98[ASN][1000 genomes]
rs62292202	0.98[ASN][1000 genomes]
rs6446550	0.83[ASN][1000 genomes]
rs6446551	0.83[ASN][1000 genomes]
rs6446552	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6831368	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6831590	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6834007	0.84[ASN][1000 genomes]
rs6848114	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7664348	0.92[ASN][1000 genomes]
rs7668186	0.88[ASN][1000 genomes]
rs7668673	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7689337	0.83[ASN][1000 genomes]
rs9291121	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs9291123	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9291124	0.98[ASN][1000 genomes]
rs9790586	0.89[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9999025	0.92[ASN][1000 genomes]
rs9999127	0.88[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	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6926200-6943200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:6928000-6969600	Weak transcription	Aorta	Aorta
3	chr4:6929800-6943200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:6931400-6943200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr4:6932000-6943400	Weak transcription	Fetal Brain Female	brain
6	chr4:6932000-6943400	Weak transcription	Fetal Kidney	kidney
7	chr4:6932200-6943200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:6934400-6946400	Enhancers	Placenta	Placenta
9	chr4:6935400-6943200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:6936000-6943200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:6939000-6945600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr4:6939000-6946800	Enhancers	Adipose Nuclei	Adipose
13	chr4:6939200-6943200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr4:6939200-6943200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:6939200-6943400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:6939200-6943400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr4:6939200-6943800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:6939200-6946200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:6939200-6947000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr4:6939200-6947200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr4:6939200-6948000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr4:6939400-6943400	Enhancers	Primary B cells from cord blood	blood
23	chr4:6939400-6943600	Enhancers	Primary hematopoietic stem cells	blood
24	chr4:6939400-6943800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:6939400-6944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr4:6939400-6945600	Enhancers	Primary B cells from peripheral blood	blood
27	chr4:6939600-6947000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:6939800-6945000	Enhancers	Brain Cingulate Gyrus	brain
29	chr4:6940400-6943200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:6940600-6943000	Weak transcription	Lung	lung
31	chr4:6940600-6943200	Weak transcription	HUVEC	blood vessel
32	chr4:6940600-6946400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr4:6940800-6943200	Enhancers	Primary T cells from cord blood	blood
34	chr4:6940800-6943200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr4:6940800-6944000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:6941000-6943200	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr4:6941000-6943200	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr4:6941000-6944000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:6941200-6943200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr4:6941200-6943400	Enhancers	Primary T cells fromperipheralblood	blood
41	chr4:6941200-6945400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:6941200-6945800	Enhancers	Spleen	Spleen
43	chr4:6941400-6943200	Weak transcription	Brain Angular Gyrus	brain
44	chr4:6941400-6943200	Weak transcription	Fetal Heart	heart
45	chr4:6941400-6943400	Enhancers	Duodenum Mucosa	Duodenum
46	chr4:6941400-6943600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:6941400-6943800	Genic enhancers	Fetal Intestine Small	intestine
48	chr4:6941400-6944000	Enhancers	K562	blood
49	chr4:6941400-6946400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr4:6941400-6946400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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