Variant report

Variant	rs339683
Chromosome Location	chr3:42788511-42788512
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	chr3:42787545..42791354-chr3:42791558..42794985,4	K562	blood:
2	chr3:42695894..42698650-chr3:42786338..42788734,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs121993	1.00[YRI][hapmap];0.94[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];0.94[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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339662	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339682	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	0.94[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];0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs339683	FHL1	trans	lymphoblastoid	seeQTL
rs339683	HIGD1A	cis	parietal	SCAN
rs339683	HHATL	cis	parietal	SCAN
rs339683	HHATL	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42781000-42788600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr3:42781200-42788600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr3:42781800-42802800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:42785200-42790200	Enhancers	Brain Anterior Caudate	brain
6	chr3:42785200-42792000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:42785200-42792000	Enhancers	Brain Substantia Nigra	brain
8	chr3:42785400-42788800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:42785400-42790200	Enhancers	Brain Hippocampus Middle	brain
10	chr3:42785400-42792000	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:42785600-42790200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:42785600-42791600	Enhancers	Rectal Smooth Muscle	rectum
13	chr3:42785600-42791800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr3:42785800-42791800	Enhancers	Fetal Muscle Leg	muscle
15	chr3:42786400-42788600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:42786400-42788800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:42786400-42789400	Enhancers	Placenta	Placenta
18	chr3:42786400-42790200	Enhancers	Fetal Stomach	stomach
19	chr3:42786600-42788800	Enhancers	Right Atrium	heart
20	chr3:42786600-42789000	Enhancers	Fetal Lung	lung
21	chr3:42786600-42790000	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr3:42786600-42790400	Enhancers	Brain Angular Gyrus	brain
23	chr3:42786800-42788600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:42787000-42789000	Enhancers	Psoas Muscle	Psoas
25	chr3:42787000-42789200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:42787200-42789000	Enhancers	Fetal Brain Female	brain
27	chr3:42787200-42789000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr3:42787200-42790000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:42787400-42788600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:42787400-42788600	Enhancers	Fetal Brain Male	brain
31	chr3:42787400-42788600	Enhancers	Ovary	ovary
32	chr3:42787400-42788800	Enhancers	Left Ventricle	heart
33	chr3:42787400-42788800	Enhancers	Right Ventricle	heart
34	chr3:42787400-42788800	Weak transcription	NHEK	skin
35	chr3:42787400-42789000	Enhancers	Aorta	Aorta
36	chr3:42787400-42789400	Enhancers	Lung	lung
37	chr3:42787400-42790000	Enhancers	Esophagus	oesophagus
38	chr3:42787400-42790800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:42787400-42791800	Enhancers	Fetal Muscle Trunk	muscle
40	chr3:42787600-42788600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:42787600-42788600	Enhancers	Adipose Nuclei	Adipose
42	chr3:42787600-42788600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr3:42787600-42788800	Enhancers	Gastric	stomach
44	chr3:42787600-42789000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:42787600-42789000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:42787600-42789800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:42787800-42788600	Enhancers	Liver	Liver
48	chr3:42787800-42788600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr3:42787800-42788800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr3:42787800-42789000	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links