Variant report

Variant	rs2841568
Chromosome Location	chr6:13458860-13458861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13450822..13452338-chr6:13457314..13458935,2	K562	blood:
2	chr6:13458838..13461788-chr6:13485026..13487935,2	MCF-7	breast:
3	chr6:13458780..13460333-chr6:13460354..13463119,2	MCF-7	breast:
4	chr6:13453145..13455587-chr6:13457422..13460283,2	K562	blood:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000145990	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10948701	0.91[AFR][1000 genomes]
rs2434395	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs2560760	0.93[YRI][hapmap];0.89[AFR][1000 genomes]
rs9395801	0.91[AFR][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:87 , 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	chr6:13445600-13461800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr6:13449000-13461800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:13452000-13462000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:13452200-13483400	Weak transcription	Gastric	stomach
6	chr6:13452400-13460800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:13453400-13461800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:13453800-13459000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr6:13453800-13459200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:13454000-13459400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:13454400-13461800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr6:13454400-13485000	Weak transcription	Colonic Mucosa	Colon
13	chr6:13455200-13462600	Weak transcription	Stomach Mucosa	stomach
14	chr6:13455200-13466600	Weak transcription	Pancreas	Pancrea
15	chr6:13455200-13484400	Weak transcription	Small Intestine	intestine
16	chr6:13455200-13484600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:13455400-13462000	Weak transcription	Esophagus	oesophagus
18	chr6:13455400-13462600	Weak transcription	HSMM	muscle
19	chr6:13455400-13463200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:13455400-13481000	Weak transcription	HUVEC	blood vessel
21	chr6:13455600-13459000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:13455600-13462000	Weak transcription	NHDF-Ad	bronchial
23	chr6:13455800-13461200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr6:13455800-13462000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:13456000-13459400	Enhancers	GM12878-XiMat	blood
26	chr6:13456200-13461400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:13456200-13461400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:13456200-13461400	Weak transcription	Aorta	Aorta
29	chr6:13456200-13461400	Weak transcription	Lung	lung
30	chr6:13456200-13461600	Weak transcription	Primary T cells from cord blood	blood
31	chr6:13456200-13462000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr6:13456200-13462000	Weak transcription	Dnd41	blood
33	chr6:13456200-13463000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:13456200-13463000	Weak transcription	Fetal Brain Female	brain
35	chr6:13456200-13464400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr6:13456200-13466200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:13456400-13461600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr6:13456400-13461800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr6:13456600-13467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:13457000-13459200	Enhancers	Brain Substantia Nigra	brain
41	chr6:13457200-13459000	Enhancers	Spleen	Spleen
42	chr6:13457200-13459400	Enhancers	Psoas Muscle	Psoas
43	chr6:13457200-13462000	Weak transcription	Thymus	Thymus
44	chr6:13457400-13461400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:13457400-13461600	Weak transcription	Primary B cells from cord blood	blood
46	chr6:13457400-13462000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:13457600-13461400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr6:13457600-13461400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr6:13457600-13461800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:13457800-13459000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links