Variant report

Variant	rs17002804
Chromosome Location	chr4:78708696-78708697
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78708609..78711608-chr4:78711846..78715407,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10005531	0.94[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[YRI][hapmap]
rs10005935	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10018117	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10019920	0.85[CHB][hapmap]
rs10026176	0.94[ASW][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes]
rs11931686	0.85[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11942975	0.83[AMR][1000 genomes]
rs12509847	0.85[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs13131331	0.83[AMR][1000 genomes]
rs1587563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1809919	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996740	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs28436599	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28685099	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4128860	0.94[ASW][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap]
rs4859512	0.85[CHB][hapmap]
rs4859513	0.85[CHB][hapmap]
rs4859882	0.90[CHB][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4859884	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs4859890	0.89[YRI][hapmap]
rs6533225	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67814821	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6811439	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6816134	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6825492	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6835993	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6849145	0.94[CHD][hapmap];0.81[GIH][hapmap]
rs7660788	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7682450	0.85[CHB][hapmap];0.83[AMR][1000 genomes]
rs7698009	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs924684	0.85[CHB][hapmap]
rs9654194	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9994366	0.80[AFR][1000 genomes];0.83[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	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17002804	G3BP2	cis	parietal	SCAN
rs17002804	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL
rs17002804	BTC	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78643800-78714000	Weak transcription	Lung	lung
2	chr4:78650200-78720000	Weak transcription	Spleen	Spleen
3	chr4:78694200-78722000	Weak transcription	Fetal Stomach	stomach
4	chr4:78696400-78717600	Weak transcription	Thymus	Thymus
5	chr4:78697200-78716400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:78697400-78721400	Weak transcription	Placenta	Placenta
7	chr4:78697600-78709200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr4:78698000-78714000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:78698000-78714600	Weak transcription	Fetal Thymus	thymus
10	chr4:78698000-78716400	Weak transcription	Primary B cells from cord blood	blood
11	chr4:78698600-78710600	Weak transcription	Left Ventricle	heart
12	chr4:78698600-78710600	Weak transcription	Ovary	ovary
13	chr4:78698600-78710800	Weak transcription	Adipose Nuclei	Adipose
14	chr4:78698600-78714000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:78698600-78717400	Weak transcription	Right Ventricle	heart
16	chr4:78698600-78720200	Weak transcription	Dnd41	blood
17	chr4:78698800-78710000	Weak transcription	Liver	Liver
18	chr4:78698800-78717400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:78699200-78716400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:78699400-78714000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:78701600-78716600	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr4:78701600-78721400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:78701800-78712400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr4:78702600-78711400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr4:78702800-78709200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:78703600-78718000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr4:78703800-78710200	Weak transcription	Small Intestine	intestine
28	chr4:78704400-78710000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:78704800-78716600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:78704800-78716600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:78704800-78722200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:78705000-78710200	Weak transcription	HepG2	liver
33	chr4:78705800-78709200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:78705800-78720000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:78706000-78710600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:78706000-78710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:78706000-78717600	Weak transcription	Right Atrium	heart
38	chr4:78706200-78719800	Weak transcription	Fetal Intestine Small	intestine
39	chr4:78707000-78711200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr4:78707000-78716600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr4:78707200-78710200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr4:78707400-78720200	Weak transcription	Gastric	stomach
43	chr4:78707600-78709000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:78707600-78709000	Weak transcription	Primary T cells from cord blood	blood
45	chr4:78707600-78717800	Weak transcription	Esophagus	oesophagus
46	chr4:78707800-78712000	Weak transcription	Psoas Muscle	Psoas
47	chr4:78708000-78709600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr4:78708000-78716400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr4:78708200-78709000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:78708200-78710600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links