Variant report

Variant	rs6665542
Chromosome Location	chr1:47909297-47909298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47643392..47645618-chr1:47908506..47910318,2	K562	blood:

Variant related genes	Relation type
ENSG00000224805	Chromatin interaction
ENSG00000225506	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1765156	0.83[AFR][1000 genomes]
rs2622916	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2820966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs472993	0.89[AFR][1000 genomes]
rs479363	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4926868	0.89[AFR][1000 genomes]
rs495482	0.83[AFR][1000 genomes]
rs506329	0.89[AFR][1000 genomes]
rs522768	0.89[AFR][1000 genomes]
rs527133	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs527430	0.89[AFR][1000 genomes]
rs557101	0.83[AFR][1000 genomes]
rs567097	1.00[AMR][1000 genomes]
rs6676787	1.00[AMR][1000 genomes]
rs9436456	0.89[AFR][1000 genomes]
rs9436902	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2755190	chr1:47907580-48048680	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47904800-47910000	Weak transcription	Pancreas	Pancrea
2	chr1:47906000-47910000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
3	chr1:47907600-47918400	Weak transcription	Aorta	Aorta
4	chr1:47908800-47909400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr1:47908800-47909400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr1:47908800-47909800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr1:47908800-47909800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:47908800-47911200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
9	chr1:47909000-47909400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr1:47909000-47910200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr1:47909000-47910400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:47909000-47910600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:47909000-47911200	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr1:47909000-47912000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:47909200-47909400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr1:47909200-47909400	Bivalent Enhancer	Thymus	Thymus
17	chr1:47909200-47909600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
18	chr1:47909200-47909600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr1:47909200-47909600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
20	chr1:47909200-47909600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
21	chr1:47909200-47909600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr1:47909200-47910000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr1:47909200-47910000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:47909200-47910000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
25	chr1:47909200-47910000	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr1:47909200-47910200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:47909200-47910200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:47909200-47910200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:47909200-47910400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr1:47909200-47910400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
31	chr1:47909200-47910400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:47909200-47910400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
33	chr1:47909200-47910600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr1:47909200-47910600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
35	chr1:47909200-47911000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links