Variant report

Variant	rs3822870
Chromosome Location	chr6:75990575-75990576
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	FOXA2	chr6:75990111-75990586	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:75988245..75991323-chr6:76311597..76315056,3	MCF-7	breast:
2	chr6:75985223..75988429-chr6:75989694..75991807,3	MCF-7	breast:
3	chr6:75987095..75989976-chr6:75990032..75992457,3	MCF-7	breast:
4	chr6:75949965..75952102-chr6:75989407..75991493,2	K562	blood:

Variant related genes	Relation type
ENSG00000225793	TF binding region
ENSG00000112701	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs15616	0.81[ASN][1000 genomes]
rs16886197	1.00[CEU][hapmap]
rs16886390	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs16886391	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs16886411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1831689	1.00[EUR][1000 genomes]
rs2300791	1.00[CEU][hapmap]
rs2300794	1.00[CEU][hapmap]
rs240374	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs240388	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs240390	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs240392	0.81[ASN][1000 genomes]
rs240423	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs240432	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2703710	0.82[JPT][hapmap]
rs2808191	0.82[JPT][hapmap]
rs2808196	0.82[JPT][hapmap]
rs2842457	0.82[JPT][hapmap]
rs2951933	0.82[JPT][hapmap]
rs2951935	0.81[JPT][hapmap]
rs2951948	0.81[JPT][hapmap]
rs2951953	0.82[JPT][hapmap]
rs2998376	0.82[JPT][hapmap]
rs3756794	0.94[ASN][1000 genomes]
rs3777512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414624	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs545588	1.00[CEU][hapmap]
rs560250	1.00[CEU][hapmap]
rs658592	1.00[CEU][hapmap]
rs6927227	1.00[CEU][hapmap]
rs7741596	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75969600-75992200	Weak transcription	Colonic Mucosa	Colon
2	chr6:75970000-75992400	Weak transcription	Brain Substantia Nigra	brain
3	chr6:75974200-75993000	Weak transcription	Placenta	Placenta
4	chr6:75975000-75992400	Weak transcription	Fetal Stomach	stomach
5	chr6:75978200-75992400	Weak transcription	Fetal Kidney	kidney
6	chr6:75978600-75993600	Weak transcription	Esophagus	oesophagus
7	chr6:75982600-75991800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:75982600-75992400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:75982600-75993600	Weak transcription	Spleen	Spleen
10	chr6:75982800-75991800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:75983000-75991000	Weak transcription	Primary B cells from cord blood	blood
12	chr6:75983000-75991800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:75983000-75991800	Weak transcription	Fetal Intestine Large	intestine
14	chr6:75983000-75992400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:75983000-75992400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:75983000-75992400	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:75983000-75992400	Weak transcription	Thymus	Thymus
18	chr6:75983000-75992600	Weak transcription	Fetal Thymus	thymus
19	chr6:75983000-75993200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr6:75983000-75993400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:75983200-75991800	Weak transcription	Aorta	Aorta
22	chr6:75984000-75991200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:75984400-75991600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:75985200-75990800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:75985400-75990600	Enhancers	NH-A	brain
26	chr6:75986200-75991400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:75986400-75991400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:75986400-75992400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:75987000-75990800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:75987400-75993600	Weak transcription	Lung	lung
31	chr6:75987600-75992400	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:75987600-75992600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:75987800-75992000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:75987800-75992400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:75987800-75996200	Active TSS	GM12878-XiMat	blood
36	chr6:75988000-75991800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr6:75988000-75992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:75988000-75993000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr6:75988000-75993000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr6:75988000-75993200	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:75988000-75993200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:75988200-75991600	Enhancers	NHEK	skin
43	chr6:75988200-75992200	Enhancers	Adipose Nuclei	Adipose
44	chr6:75988200-75992400	Enhancers	Fetal Brain Male	brain
45	chr6:75988200-75993000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:75988400-75991200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr6:75988400-75991400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:75988400-75991600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:75988400-75991800	Weak transcription	Ovary	ovary
50	chr6:75988400-75992400	Weak transcription	H9 Cell Line	embryonic stem cell

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