Variant report

Variant	rs6551281
Chromosome Location	chr3:88208201-88208202
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88197769..88200999-chr3:88203234..88208947,7	MCF-7	breast:
2	chr3:88197032..88201570-chr3:88203720..88209497,8	K562	blood:
3	chr3:88207610..88209818-chr3:88212134..88214341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1006896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10858	0.87[ASN][1000 genomes]
rs11925988	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493327	1.00[JPT][hapmap]
rs13074910	1.00[CEU][hapmap]
rs13317202	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2735559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4858934	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858939	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858940	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859003	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883959	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55928667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211058	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246133	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419868	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419869	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551295	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73132512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132546	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146085	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146095	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146099	0.87[ASN][1000 genomes]
rs73148006	0.80[ASN][1000 genomes]
rs7430022	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7431968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7432826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432838	1.00[JPT][hapmap]
rs7610494	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620576	0.89[EUR][1000 genomes]
rs7620830	1.00[JPT][hapmap]
rs7624215	0.91[EUR][1000 genomes]
rs7650068	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284814	0.87[EUR][1000 genomes]
rs9826925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv3352726	chr3:88208142-88208346	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6551281	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs6551281	CGGBP1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
2	chr3:88200800-88209400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:88200800-88214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
5	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
6	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
7	chr3:88201200-88209600	Weak transcription	Stomach Mucosa	stomach
8	chr3:88201400-88212200	Weak transcription	Colonic Mucosa	Colon
9	chr3:88202000-88208400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:88202000-88210200	Strong transcription	Placenta	Placenta
11	chr3:88202000-88211400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:88202200-88209200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:88202200-88211000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:88202200-88211800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:88202200-88212000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:88202400-88208400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:88202400-88208600	Strong transcription	Fetal Thymus	thymus
18	chr3:88202400-88208800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:88202400-88210000	Strong transcription	Liver	Liver
20	chr3:88202600-88208400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:88202600-88209000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:88202600-88211000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:88202600-88211200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:88202800-88208400	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:88202800-88208600	Strong transcription	Adipose Nuclei	Adipose
26	chr3:88202800-88212600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:88203000-88208400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:88203000-88212200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:88203000-88214200	Weak transcription	Small Intestine	intestine
30	chr3:88203400-88208400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:88203600-88208600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr3:88203800-88208400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:88204200-88208600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:88204200-88208600	Strong transcription	NHLF	lung
35	chr3:88204200-88212400	Strong transcription	Primary B cells from peripheral blood	blood
36	chr3:88204400-88217400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr3:88205000-88209200	Strong transcription	Primary B cells from cord blood	blood
38	chr3:88205000-88213800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:88205200-88208600	Strong transcription	K562	blood
40	chr3:88205600-88212400	Weak transcription	Gastric	stomach
41	chr3:88205600-88217600	Weak transcription	Fetal Intestine Small	intestine
42	chr3:88205600-88222000	Weak transcription	Fetal Stomach	stomach
43	chr3:88205600-88222800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:88205800-88208400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:88205800-88209800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:88205800-88217800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:88205800-88220200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:88205800-88227000	Weak transcription	Lung	lung
49	chr3:88205800-88232400	Weak transcription	Left Ventricle	heart
50	chr3:88206000-88208800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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