Variant report

Variant	rs2841564
Chromosome Location	chr6:13455989-13455990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13454821..13457095-chr6:13613822..13616173,2	MCF-7	breast:
2	chr6:13447200..13448830-chr6:13453406..13456212,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1863995	0.97[EUR][1000 genomes]
rs2560757	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560759	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560761	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841560	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2841565	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13438600-13462200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:13445200-13457800	Enhancers	Right Atrium	heart
3	chr6:13445600-13461800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:13448200-13458200	Enhancers	Colon Smooth Muscle	Colon
5	chr6:13449000-13457200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:13449000-13461800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:13451800-13458600	Weak transcription	HepG2	liver
8	chr6:13452000-13456400	Enhancers	Fetal Stomach	stomach
9	chr6:13452000-13456600	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr6:13452000-13462000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:13452200-13483400	Weak transcription	Gastric	stomach
12	chr6:13452400-13460800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:13452800-13457000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:13453200-13456200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:13453400-13456200	Enhancers	NH-A	brain
16	chr6:13453400-13461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr6:13453800-13456200	Enhancers	HMEC	breast
18	chr6:13453800-13456400	Enhancers	Fetal Heart	heart
19	chr6:13453800-13458800	Enhancers	Left Ventricle	heart
20	chr6:13453800-13459000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:13453800-13459200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:13454000-13456200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:13454000-13456200	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr6:13454000-13456200	Enhancers	Spleen	Spleen
25	chr6:13454000-13456200	Enhancers	Dnd41	blood
26	chr6:13454000-13456400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:13454000-13456600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:13454000-13456600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:13454000-13457400	Enhancers	Primary hematopoietic stem cells	blood
30	chr6:13454000-13457800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr6:13454000-13457800	Enhancers	Fetal Thymus	thymus
32	chr6:13454000-13458200	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:13454000-13458200	Enhancers	Adipose Nuclei	Adipose
34	chr6:13454000-13458200	Enhancers	Brain Cingulate Gyrus	brain
35	chr6:13454000-13459400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:13454200-13456000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr6:13454200-13456200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:13454200-13456200	Enhancers	Lung	lung
39	chr6:13454200-13456200	Enhancers	Psoas Muscle	Psoas
40	chr6:13454200-13458400	Enhancers	Right Ventricle	heart
41	chr6:13454400-13456000	Flanking Active TSS	GM12878-XiMat	blood
42	chr6:13454400-13456400	Enhancers	Primary B cells from cord blood	blood
43	chr6:13454400-13456400	Enhancers	Liver	Liver
44	chr6:13454400-13461800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
46	chr6:13454600-13456200	Enhancers	Fetal Brain Male	brain
47	chr6:13454800-13456200	Enhancers	K562	blood
48	chr6:13455200-13456000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr6:13455200-13456200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr6:13455200-13456400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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