Variant report

Variant	rs3804454
Chromosome Location	chr6:36006998-36006999
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35995194..35998195-chr6:36005882..36008273,3	MCF-7	breast:
2	chr6:36005811..36007501-chr6:36031896..36034665,2	MCF-7	breast:
3	chr6:36004256..36008488-chr6:36021572..36023371,4	K562	blood:
4	chr6:36006492..36008488-chr6:36021459..36023268,2	K562	blood:
5	chr6:36005324..36007275-chr6:36062983..36064976,2	K562	blood:

Variant related genes	Relation type
ENSG00000112062	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs16883860	0.93[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs16883989	0.88[AFR][1000 genomes]
rs16884628	0.86[LWK][hapmap]
rs16884906	0.81[AFR][1000 genomes]
rs2237094	0.88[LWK][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs3730366	0.91[LWK][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs3761980	0.86[LWK][hapmap]
rs3804451	0.82[LWK][hapmap]
rs56059109	0.88[AFR][1000 genomes]
rs56362075	0.83[AFR][1000 genomes]
rs58632953	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60100837	0.87[AFR][1000 genomes]
rs61364424	0.83[AFR][1000 genomes]
rs6457878	0.82[LWK][hapmap]
rs6908622	0.88[AFR][1000 genomes]
rs6910685	0.83[AFR][1000 genomes]
rs6921999	0.88[AFR][1000 genomes]
rs6930333	0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs6934216	0.83[AFR][1000 genomes]
rs73407870	0.88[AFR][1000 genomes]
rs73407871	0.88[AFR][1000 genomes]
rs73409842	0.88[AFR][1000 genomes]
rs73729698	0.83[AFR][1000 genomes]
rs73730437	0.88[AFR][1000 genomes]
rs73730440	0.83[AFR][1000 genomes]
rs7745536	0.87[YRI][hapmap];0.88[AFR][1000 genomes]
rs7745927	0.88[AFR][1000 genomes]
rs7759175	0.83[AFR][1000 genomes]
rs7760578	0.88[AFR][1000 genomes]
rs7761118	0.86[LWK][hapmap];0.83[YRI][hapmap]
rs7775290	0.86[YRI][hapmap];0.87[AFR][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	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv528432	chr6:35958871-36035354	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3804454	SLC26A8	cis	parietal	SCAN
rs3804454	FKBP5	cis	parietal	SCAN
rs3804454	MAPK14	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35997600-36008800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr6:35997600-36010800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:35997600-36021800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:35998000-36007400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr6:35998000-36019200	Weak transcription	HSMM	muscle
6	chr6:35998200-36018400	Weak transcription	NHLF	lung
7	chr6:35998200-36018600	Weak transcription	NHDF-Ad	bronchial
8	chr6:35998600-36007400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr6:35998800-36008800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:35999000-36027600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:36000600-36009800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:36000600-36020400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:36000600-36027400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:36000800-36009200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:36003200-36027200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:36003600-36007000	Weak transcription	Brain Substantia Nigra	brain
17	chr6:36003800-36014600	Weak transcription	Gastric	stomach
18	chr6:36003800-36027600	Weak transcription	Colonic Mucosa	Colon
19	chr6:36004800-36008600	Enhancers	Primary T cells from cord blood	blood
20	chr6:36005000-36008000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr6:36005000-36008800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:36005000-36008800	Enhancers	Colon Smooth Muscle	Colon
23	chr6:36005000-36009200	Enhancers	HepG2	liver
24	chr6:36005000-36009400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:36005000-36010200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:36005200-36007400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:36005200-36008600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:36005200-36008800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr6:36005200-36008800	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:36005200-36009400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr6:36005400-36007200	Enhancers	Primary B cells from cord blood	blood
32	chr6:36005400-36007200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:36005400-36007200	Enhancers	Adipose Nuclei	Adipose
34	chr6:36005400-36007200	Enhancers	Duodenum Mucosa	Duodenum
35	chr6:36005400-36007200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr6:36005400-36007600	Enhancers	Liver	Liver
37	chr6:36005400-36008600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:36005400-36008600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:36005400-36020400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:36005600-36007200	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr6:36005600-36007200	Enhancers	K562	blood
42	chr6:36005600-36007400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr6:36005600-36007400	Enhancers	Brain Hippocampus Middle	brain
44	chr6:36005600-36007400	Enhancers	Fetal Lung	lung
45	chr6:36005600-36008000	Enhancers	Small Intestine	intestine
46	chr6:36005800-36007200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:36005800-36007400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:36005800-36007400	Enhancers	Fetal Heart	heart
49	chr6:36005800-36008800	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr6:36005800-36009000	Enhancers	NHEK	skin

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