Variant report

Variant	rs6840339
Chromosome Location	chr4:119748295-119748296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119748060..119751359-chr4:119755733..119758642,4	MCF-7	breast:
2	chr4:119746389..119748535-chr4:119756250..119758555,2	MCF-7	breast:
3	chr4:119746430..119750186-chr4:119793927..119797109,3	K562	blood:
4	chr4:119734323..119737022-chr4:119746808..119748529,2	K562	blood:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11098452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11731153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1426813	0.84[MEX][hapmap]
rs3775834	0.87[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4586912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4834707	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6822035	0.86[CHB][hapmap]
rs6828577	0.82[CHB][hapmap]
rs6843239	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv516777	chr4:119733366-119762951	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6840339	SYNPO2	cis	cerebellum	SCAN
rs6840339	USP53	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119718400-119756000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:119718600-119753600	Weak transcription	Fetal Heart	heart
3	chr4:119719000-119756200	Weak transcription	Fetal Brain Male	brain
4	chr4:119732000-119755800	Weak transcription	Brain Angular Gyrus	brain
5	chr4:119733400-119753200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:119734800-119755800	Weak transcription	Thymus	Thymus
7	chr4:119735600-119756000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:119735600-119756200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:119735800-119751400	Weak transcription	Fetal Brain Female	brain
10	chr4:119736400-119756200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:119736800-119753000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:119736800-119755800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:119736800-119756200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:119736800-119756200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:119736800-119756200	Weak transcription	Brain Substantia Nigra	brain
16	chr4:119737000-119755800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:119737000-119756000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:119737200-119752400	Weak transcription	Fetal Kidney	kidney
19	chr4:119737800-119752400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:119744800-119753400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr4:119744800-119753400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr4:119744800-119755800	Weak transcription	Brain Hippocampus Middle	brain
23	chr4:119745200-119753400	Weak transcription	Spleen	Spleen
24	chr4:119745200-119755400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:119745400-119754800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:119745800-119748600	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr4:119745800-119752200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:119746000-119748600	Weak transcription	Pancreas	Pancrea
29	chr4:119746000-119750000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:119746000-119750000	Weak transcription	Fetal Thymus	thymus
31	chr4:119746000-119752800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:119746000-119753000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:119746000-119753400	Weak transcription	Colonic Mucosa	Colon
34	chr4:119746000-119753600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr4:119746000-119754800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr4:119746200-119748600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:119746200-119754800	Weak transcription	Small Intestine	intestine
38	chr4:119746400-119752200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:119746600-119748400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr4:119746600-119749400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:119746600-119749400	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:119746600-119749400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:119746600-119749600	Weak transcription	Primary T cells from cord blood	blood
44	chr4:119746600-119749600	Weak transcription	Placenta	Placenta
45	chr4:119746600-119749600	Weak transcription	Dnd41	blood
46	chr4:119746600-119749600	Weak transcription	NHEK	skin
47	chr4:119746600-119750000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:119746600-119752600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:119746600-119753400	Weak transcription	Primary B cells from cord blood	blood
50	chr4:119746800-119748400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links