Variant report

Variant	rs774004
Chromosome Location	chr3:138177132-138177133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1082037	0.81[ASN][1000 genomes]
rs1088055	0.81[ASN][1000 genomes]
rs10935284	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13101081	0.93[ASN][1000 genomes]
rs1379257	0.81[ASN][1000 genomes]
rs1479930	0.93[ASN][1000 genomes]
rs1600511	0.93[ASN][1000 genomes]
rs1630766	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1673593	0.81[ASN][1000 genomes]
rs1679167	0.93[ASN][1000 genomes]
rs1679168	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1679175	0.84[ASN][1000 genomes]
rs1720836	0.93[ASN][1000 genomes]
rs2347469	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2881793	0.81[ASN][1000 genomes]
rs4432674	0.81[ASN][1000 genomes]
rs4678264	0.93[ASN][1000 genomes]
rs4678265	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4678420	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs550507	0.81[ASN][1000 genomes]
rs60513493	0.81[ASN][1000 genomes]
rs611134	0.81[ASN][1000 genomes]
rs629884	0.81[ASN][1000 genomes]
rs680070	0.81[ASN][1000 genomes]
rs7625326	0.93[ASN][1000 genomes]
rs7634745	0.93[ASN][1000 genomes]
rs7643973	0.81[ASN][1000 genomes]
rs7653815	0.93[ASN][1000 genomes]
rs773445	0.81[ASN][1000 genomes]
rs774003	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs774005	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774006	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774007	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774008	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs808925	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811792	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs811793	0.93[ASN][1000 genomes]
rs9811052	0.93[ASN][1000 genomes]
rs9817419	0.81[ASN][1000 genomes]
rs9827256	0.87[ASN][1000 genomes]
rs9848718	0.93[ASN][1000 genomes]
rs9853998	0.93[ASN][1000 genomes]
rs9878436	0.81[ASN][1000 genomes]
rs9879213	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs774004	CEP70	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 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	chr3:138162400-138177200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:138162800-138178800	Weak transcription	Fetal Intestine Small	intestine
5	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:138170800-138198400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:138171000-138193000	Weak transcription	Pancreas	Pancrea
8	chr3:138171200-138185400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:138171400-138198400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:138172400-138181800	Weak transcription	Placenta	Placenta
11	chr3:138173800-138179000	Strong transcription	Lung	lung
12	chr3:138173800-138181200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:138174200-138180800	Enhancers	Fetal Muscle Trunk	muscle
14	chr3:138174600-138183600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:138174800-138177800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:138175200-138178600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:138175200-138180400	Weak transcription	Osteobl	bone
18	chr3:138175200-138196000	Weak transcription	Brain Anterior Caudate	brain
19	chr3:138175400-138178400	Weak transcription	Right Atrium	heart
20	chr3:138175400-138179600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:138175400-138180000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:138175600-138177600	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:138175800-138178000	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr3:138175800-138178600	Strong transcription	Fetal Stomach	stomach
25	chr3:138176200-138177800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:138176200-138178000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:138176400-138177800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr3:138176400-138180000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:138176400-138180600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr3:138176400-138184800	Genic enhancers	Fetal Muscle Leg	muscle
31	chr3:138176600-138177600	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:138176600-138177600	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:138176800-138177200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
34	chr3:138176800-138178000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:138176800-138179600	Weak transcription	HSMMtube	muscle
36	chr3:138176800-138187200	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links