Variant report

Variant	rs6777622
Chromosome Location	chr3:99787982-99787983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99535064..99536649-chr3:99785344..99788184,2	K562	blood:
2	chr3:99787221..99788265-chr3:99972698..99973390,5	K562	blood:
3	chr3:99603110..99605515-chr3:99787025..99789865,2	MCF-7	breast:
4	chr3:99787458..99788080-chr3:99967948..99968860,2	MCF-7	breast:
5	chr3:99787349..99788508-chr3:99972741..99973631,4	MCF-7	breast:
6	chr3:99787292..99788466-chr3:99972325..99973638,6	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12486901	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12489030	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12494994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496041	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1387649	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3921767	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs4928233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928240	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414382	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440992	0.82[AMR][1000 genomes]
rs6778589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792339	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6800456	0.85[JPT][hapmap]
rs73859922	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632345	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7634628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7641782	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7652706	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs9824430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9872339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99767600-99801000	Weak transcription	HSMM	muscle
2	chr3:99768400-99788000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99774000-99794800	Weak transcription	Stomach Mucosa	stomach
4	chr3:99783200-99792400	Weak transcription	Psoas Muscle	Psoas
5	chr3:99783200-99793600	Weak transcription	Aorta	Aorta
6	chr3:99783400-99791400	Enhancers	HepG2	liver
7	chr3:99783600-99788200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:99783600-99788600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:99783600-99791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:99783600-99792200	Weak transcription	Fetal Lung	lung
11	chr3:99784200-99791400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:99784200-99792400	Weak transcription	Fetal Stomach	stomach
13	chr3:99784400-99789400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:99785800-99788000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:99785800-99788000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr3:99786000-99788200	Enhancers	Fetal Intestine Large	intestine
17	chr3:99786800-99790400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:99786800-99790400	Weak transcription	Small Intestine	intestine
19	chr3:99787000-99792200	Weak transcription	Fetal Intestine Small	intestine
20	chr3:99787400-99788000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:99787600-99788200	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:99787600-99788400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:99787600-99788400	Enhancers	Fetal Muscle Leg	muscle
24	chr3:99787600-99788400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr3:99787600-99795200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:99787800-99788000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:99787800-99788000	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:99787800-99788000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:99787800-99788000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:99787800-99788000	Active TSS	Colon Smooth Muscle	Colon
31	chr3:99787800-99788000	Enhancers	Fetal Muscle Trunk	muscle
32	chr3:99787800-99788000	Enhancers	K562	blood
33	chr3:99787800-99788200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr3:99787800-99788200	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr3:99787800-99788200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr3:99787800-99788200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:99787800-99788200	Enhancers	Liver	Liver
38	chr3:99787800-99788200	Enhancers	Brain Cingulate Gyrus	brain
39	chr3:99787800-99788200	Enhancers	Fetal Heart	heart
40	chr3:99787800-99788200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:99787800-99788200	Enhancers	Fetal Thymus	thymus
42	chr3:99787800-99788200	Enhancers	Thymus	Thymus
43	chr3:99787800-99788200	Enhancers	GM12878-XiMat	blood
44	chr3:99787800-99788200	Enhancers	NHLF	lung
45	chr3:99787800-99788400	Enhancers	Primary T cells from cord blood	blood
46	chr3:99787800-99788400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:99787800-99788400	Enhancers	Adipose Nuclei	Adipose
48	chr3:99787800-99788400	Enhancers	Brain Anterior Caudate	brain
49	chr3:99787800-99788400	Enhancers	Ovary	ovary
50	chr3:99787800-99788400	Enhancers	Rectal Mucosa Donor 31	rectum

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