Variant report

Variant	rs6860252
Chromosome Location	chr5:14411621-14411622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14406629..14408543-chr5:14409442..14412662,3	K562	blood:
2	chr5:14407542..14409626-chr5:14411209..14413793,2	MCF-7	breast:
3	chr5:14407920..14412107-chr5:14413885..14416299,3	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10056415	0.97[EUR][1000 genomes]
rs10078445	0.97[EUR][1000 genomes]
rs12332644	0.97[EUR][1000 genomes]
rs16903421	0.88[MEX][hapmap]
rs16903453	0.82[ASW][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap]
rs16903497	0.93[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56207939	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57640930	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs59371168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60123555	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60534900	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60871697	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62345046	0.93[EUR][1000 genomes]
rs6860137	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6883134	1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6887662	0.93[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6894866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73061636	0.97[AFR][1000 genomes];0.92[AMR][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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
2	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
5	chr5:14393600-14413600	Strong transcription	Primary B cells from cord blood	blood
6	chr5:14399000-14419800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:14399600-14416400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr5:14400200-14413400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:14400600-14415000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:14400800-14416000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:14404000-14420600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:14404200-14412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:14404400-14415000	Strong transcription	Primary B cells from peripheral blood	blood
14	chr5:14404400-14428600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:14404600-14414800	Strong transcription	Brain Germinal Matrix	brain
16	chr5:14404600-14427600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:14404800-14413000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:14404800-14413400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:14404800-14414000	Strong transcription	Fetal Brain Female	brain
20	chr5:14404800-14416200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:14404800-14417200	Strong transcription	HSMMtube	muscle
22	chr5:14404800-14424000	Strong transcription	Liver	Liver
23	chr5:14405000-14413600	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:14405200-14412400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:14405200-14413200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr5:14405200-14413400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:14405200-14415600	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:14405200-14423600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:14405400-14413000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr5:14405400-14416000	Strong transcription	Lung	lung
31	chr5:14405400-14423400	Strong transcription	Placenta	Placenta
32	chr5:14405800-14413400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr5:14406000-14411800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:14406200-14413400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr5:14406200-14416200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr5:14406400-14416200	Strong transcription	Hela-S3	cervix
37	chr5:14406600-14412800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:14406600-14414400	Strong transcription	NHLF	lung
39	chr5:14406800-14420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:14406800-14421600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:14407000-14416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr5:14407000-14417000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:14407200-14416400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:14407200-14418800	Strong transcription	NHEK	skin
45	chr5:14407600-14412000	Weak transcription	Small Intestine	intestine
46	chr5:14407600-14412400	Weak transcription	Primary T cells from cord blood	blood
47	chr5:14407600-14414400	Weak transcription	Fetal Brain Male	brain
48	chr5:14407600-14417000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:14407800-14412800	Weak transcription	Thymus	Thymus
50	chr5:14407800-14414600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links