Variant report

Variant	rs16876554
Chromosome Location	chr6:15506473-15506474
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	chr6:15503488..15507338-chr6:15507850..15510659,7	K562	blood:
2	chr6:15496453..15502686-chr6:15502830..15509631,7	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16876555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064099	0.85[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2076058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237110	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs3778651	0.82[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7756497	0.85[CEU][hapmap]
rs9296975	0.82[CEU][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs9464792	0.85[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9654600	0.88[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS 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	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	28 gene(s)	inside rSNPs	diseases
3	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15487200-15508000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr6:15492200-15507800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:15492200-15508200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:15492200-15527000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:15492400-15527200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr6:15492600-15522200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:15492800-15515000	Strong transcription	Thymus	Thymus
8	chr6:15492800-15527000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr6:15493800-15520000	Weak transcription	Hela-S3	cervix
10	chr6:15494200-15522400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:15494600-15507400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr6:15494800-15524000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:15494800-15527000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr6:15495000-15527200	Strong transcription	Dnd41	blood
15	chr6:15495000-15529200	Strong transcription	Primary T cells from cord blood	blood
16	chr6:15495200-15508400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:15495200-15525800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr6:15495400-15508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr6:15495400-15525000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:15495800-15506800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:15496000-15507000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:15496000-15525200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:15496000-15525600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:15496000-15526600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:15496000-15528400	Strong transcription	Primary B cells from cord blood	blood
26	chr6:15496200-15508200	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr6:15496600-15506600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr6:15496600-15517000	Weak transcription	Small Intestine	intestine
29	chr6:15497400-15526600	Strong transcription	Fetal Intestine Large	intestine
30	chr6:15498400-15522600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr6:15499400-15507200	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:15500600-15524600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:15501400-15507400	Genic enhancers	Fetal Stomach	stomach
34	chr6:15501800-15506600	Enhancers	Fetal Brain Male	brain
35	chr6:15501800-15508400	Enhancers	Left Ventricle	heart
36	chr6:15502400-15509400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:15502400-15522400	Weak transcription	A549	lung
38	chr6:15502600-15506600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:15502800-15521400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:15503000-15507600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr6:15503600-15508600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr6:15503800-15507200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:15504000-15506800	Enhancers	Pancreas	Pancrea
44	chr6:15504000-15507000	Weak transcription	K562	blood
45	chr6:15504200-15506800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:15504200-15507800	Genic enhancers	Spleen	Spleen
47	chr6:15504600-15507400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:15505000-15506800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:15505000-15507400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:15505200-15506600	Genic enhancers	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links