Variant report

Variant	rs559035
Chromosome Location	chr6:44405327-44405328
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr6:44405289-44405559	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44405048..44409188-chr6:44409781..44413783,5	K562	blood:
2	chr6:44403977..44405888-chr6:44416360..44418391,2	K562	blood:

Variant related genes	Relation type
ENSG00000267849	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807300	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1293205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1293208	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1296018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1952979	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2273667	0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2297331	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2297333	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2894572	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34264814	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34753552	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4143678	0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711781	0.86[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs475426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526851	0.99[ASN][1000 genomes]
rs532492	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs545455	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548342	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557470	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566078	0.84[JPT][hapmap]
rs67182313	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6918742	0.84[CHD][hapmap]
rs6923521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6942323	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs864127	0.93[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9369488	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9395016	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9395017	0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9462984	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9462985	0.88[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9462989	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9472273	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv885858	chr6:44385441-44421240	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv885859	chr6:44385441-44422466	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv517370	chr6:44385441-44422689	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1850024	chr6:44388505-44422689	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs559035	CD2AP	cis	cerebellum	SCAN
rs559035	CDC5L	cis	parietal	SCAN
rs559035	RUNX2	cis	cerebellum	SCAN
rs559035	GPR115	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44376800-44424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:44386600-44409200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr6:44386800-44406400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:44386800-44408800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr6:44387000-44405400	Strong transcription	Primary hematopoietic stem cells	blood
6	chr6:44387000-44408000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr6:44387600-44408600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:44388400-44424400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:44388800-44409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:44390200-44409600	Weak transcription	Spleen	Spleen
11	chr6:44390200-44420200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:44391800-44409800	Weak transcription	Aorta	Aorta
13	chr6:44391800-44412600	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:44392800-44407000	Weak transcription	Ovary	ovary
15	chr6:44392800-44411800	Weak transcription	Esophagus	oesophagus
16	chr6:44393600-44411600	Weak transcription	Right Ventricle	heart
17	chr6:44394600-44407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:44394800-44410000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:44395200-44407000	Weak transcription	NHEK	skin
20	chr6:44395200-44407200	Weak transcription	HMEC	breast
21	chr6:44395400-44408800	Weak transcription	HUVEC	blood vessel
22	chr6:44396600-44407000	Weak transcription	Osteobl	bone
23	chr6:44396600-44432800	Weak transcription	Fetal Kidney	kidney
24	chr6:44397200-44409800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:44397400-44409800	Weak transcription	Fetal Brain Male	brain
26	chr6:44397800-44408600	Weak transcription	Brain Germinal Matrix	brain
27	chr6:44398200-44413400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:44398200-44413400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr6:44398400-44407000	Weak transcription	NHLF	lung
30	chr6:44398400-44407200	Weak transcription	Thymus	Thymus
31	chr6:44398400-44409800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr6:44398400-44410000	Weak transcription	Brain Anterior Caudate	brain
33	chr6:44398400-44411800	Weak transcription	Lung	lung
34	chr6:44398400-44413600	Weak transcription	Brain Angular Gyrus	brain
35	chr6:44398400-44415400	Weak transcription	Small Intestine	intestine
36	chr6:44398600-44407000	Weak transcription	Adipose Nuclei	Adipose
37	chr6:44398600-44407200	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:44398600-44407200	Weak transcription	Left Ventricle	heart
39	chr6:44398600-44407400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:44398600-44410000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:44398600-44411600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:44398600-44419600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr6:44398800-44408400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:44398800-44408800	Weak transcription	Brain Substantia Nigra	brain
45	chr6:44398800-44409200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:44399400-44405800	Strong transcription	HepG2	liver
47	chr6:44400000-44408200	Strong transcription	Primary T cells from cord blood	blood
48	chr6:44400600-44408600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:44400600-44413200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:44400800-44406600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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