Variant report

Variant	rs6763380
Chromosome Location	chr3:138179328-138179329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10935281	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10935282	0.88[ASN][1000 genomes]
rs10935287	0.80[AMR][1000 genomes]
rs11709290	0.98[ASN][1000 genomes]
rs12487652	0.80[AMR][1000 genomes]
rs12490633	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs12497070	0.80[AMR][1000 genomes]
rs12636910	0.81[CEU][hapmap]
rs13085181	0.83[EUR][1000 genomes]
rs13098789	0.81[AMR][1000 genomes]
rs1625751	0.85[ASN][1000 genomes]
rs1672927	0.85[CEU][hapmap]
rs1672928	0.85[CEU][hapmap]
rs1672932	0.85[CEU][hapmap]
rs1673608	0.85[CEU][hapmap]
rs1673622	0.85[CEU][hapmap];0.80[AMR][1000 genomes]
rs1679165	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1679167	0.81[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1679169	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1679175	0.88[EUR][1000 genomes]
rs1720833	0.85[ASN][1000 genomes]
rs1720836	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2086351	0.85[ASN][1000 genomes]
rs35471402	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813264	0.85[YRI][hapmap];0.96[ASN][1000 genomes]
rs3884240	0.85[CEU][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3884241	0.86[CEU][hapmap]
rs4678266	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4678418	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs497334	0.86[CEU][hapmap]
rs503922	0.85[CEU][hapmap]
rs529615	0.85[CEU][hapmap]
rs542010	0.81[CEU][hapmap]
rs56236670	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs564800	0.81[CEU][hapmap]
rs609797	0.85[CEU][hapmap]
rs6439809	0.86[CEU][hapmap];0.81[ASN][1000 genomes]
rs6439810	0.85[CEU][hapmap]
rs66644444	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67037472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626226	0.84[CEU][hapmap];0.81[ASN][1000 genomes]
rs7645920	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs773450	0.85[CEU][hapmap]
rs774011	0.85[ASN][1000 genomes]
rs774012	0.85[ASN][1000 genomes]
rs814022	0.85[CEU][hapmap]
rs936316	0.85[CEU][hapmap]
rs9822037	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9848718	0.81[CEU][hapmap]
rs9848938	0.98[ASN][1000 genomes]
rs9855306	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6763380	FAIM	Cis_1M	lymphoblastoid	RTeQTL
rs6763380	FAIM	cis	Muscle Skeletal	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138155000-138182800	Weak transcription	Gastric	stomach
2	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
6	chr3:138171200-138185400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:138172400-138181800	Weak transcription	Placenta	Placenta
9	chr3:138173800-138181200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:138174200-138180800	Enhancers	Fetal Muscle Trunk	muscle
11	chr3:138174600-138183600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:138175200-138180400	Weak transcription	Osteobl	bone
13	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:138175400-138179600	Weak transcription	Brain Angular Gyrus	brain
15	chr3:138175400-138180000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:138176400-138180000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:138176400-138180600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr3:138176400-138184800	Genic enhancers	Fetal Muscle Leg	muscle
19	chr3:138176800-138179600	Weak transcription	HSMMtube	muscle
20	chr3:138176800-138187200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:138177200-138179600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:138177200-138181200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:138177600-138187200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:138177600-138195400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:138178000-138180200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:138178000-138197000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:138178200-138196000	Weak transcription	Aorta	Aorta
28	chr3:138178400-138179800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:138178400-138183200	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:138178600-138179400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:138178600-138179400	Enhancers	Fetal Intestine Large	intestine
32	chr3:138178600-138181200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:138178600-138182600	Weak transcription	Fetal Stomach	stomach
34	chr3:138178600-138187000	Weak transcription	Right Atrium	heart
35	chr3:138178800-138179800	Enhancers	Fetal Intestine Small	intestine
36	chr3:138178800-138188800	Weak transcription	Right Ventricle	heart
37	chr3:138179000-138179800	Genic enhancers	Lung	lung
38	chr3:138179000-138181000	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links