Variant report

Variant	rs339682
Chromosome Location	chr3:42791123-42791124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42789944..42792627-chr3:42845601..42848096,2	K562	blood:
2	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:
3	chr3:42702115..42702691-chr3:42791094..42791699,3	MCF-7	breast:
4	chr3:42694253..42696988-chr3:42790179..42793098,2	K562	blood:
5	chr3:42781201..42784093-chr3:42790186..42792951,2	K562	blood:

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction
ENSG00000181061	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs121993	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs123506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs123509	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339662	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs6865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs735320	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7641452	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs834579	1.00[CHD][hapmap]
rs834584	1.00[CHD][hapmap]
rs9311331	1.00[CHB][hapmap]
rs9865715	1.00[CHB][hapmap]

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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs339682	HIGD1A	cis	parietal	SCAN
rs339682	HHATL	cis	brain	BrainEAC
rs339682	FHL1	trans	lymphoblastoid	seeQTL
rs339682	HHATL	cis	parietal	SCAN
rs339682	HHATL	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:42785200-42792000	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:42785200-42792000	Enhancers	Brain Substantia Nigra	brain
5	chr3:42785400-42792000	Enhancers	Brain Cingulate Gyrus	brain
6	chr3:42785600-42791600	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:42785600-42791800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:42785800-42791800	Enhancers	Fetal Muscle Leg	muscle
9	chr3:42787400-42791800	Enhancers	Fetal Muscle Trunk	muscle
10	chr3:42787800-42791200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:42788000-42792000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr3:42788200-42791800	Enhancers	Colon Smooth Muscle	Colon
13	chr3:42788200-42794400	Weak transcription	Stomach Mucosa	stomach
14	chr3:42788400-42797200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:42788600-42793400	Weak transcription	Fetal Brain Male	brain
16	chr3:42788600-42796000	Weak transcription	Adipose Nuclei	Adipose
17	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:42788800-42791200	Weak transcription	Right Atrium	heart
19	chr3:42788800-42793000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:42788800-42794400	Weak transcription	Gastric	stomach
21	chr3:42788800-42799800	Weak transcription	Left Ventricle	heart
22	chr3:42789000-42792600	Weak transcription	Fetal Lung	lung
23	chr3:42789000-42795200	Weak transcription	Aorta	Aorta
24	chr3:42789000-42795600	Weak transcription	Fetal Brain Female	brain
25	chr3:42789200-42791600	Enhancers	Primary T cells from cord blood	blood
26	chr3:42789400-42791200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:42789400-42791400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:42789400-42793000	Weak transcription	Lung	lung
29	chr3:42789600-42791400	Enhancers	HepG2	liver
30	chr3:42789600-42792000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:42790000-42791200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:42790000-42791200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:42790000-42792000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:42790200-42791200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:42790200-42791200	Weak transcription	Brain Anterior Caudate	brain
37	chr3:42790200-42791200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:42790200-42791200	Weak transcription	Fetal Stomach	stomach
39	chr3:42790200-42791400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:42790200-42791600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr3:42790200-42793200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:42790600-42791600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:42790600-42791600	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr3:42790600-42791800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:42790600-42792000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr3:42790600-42793600	Enhancers	Placenta	Placenta
47	chr3:42790800-42791400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:42790800-42791400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:42790800-42791600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:42790800-42791600	Enhancers	Colonic Mucosa	Colon

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