Variant report

Variant	rs4775124
Chromosome Location	chr15:59484107-59484108
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1032180	0.83[ASN][1000 genomes]
rs10519001	0.85[CEU][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs10851644	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs11071412	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11630106	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631348	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11632420	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12898967	0.82[AMR][1000 genomes]
rs12903377	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906742	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12916830	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17269566	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2129426	0.82[ASN][1000 genomes]
rs2306787	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2306788	0.92[CEU][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306789	0.85[ASN][1000 genomes]
rs3794494	0.96[CEU][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3794499	0.83[ASN][1000 genomes]
rs3794500	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4775128	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4775130	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56108450	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58948844	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162863	0.85[ASN][1000 genomes]
rs7169503	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs901481	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9788755	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1035868	chr15:59402426-59530594	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv833027	chr15:59474806-59608544	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4775124	GCOM1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59437800-59484400	Weak transcription	Fetal Brain Male	brain
2	chr15:59464400-59496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:59467800-59523200	Weak transcription	Fetal Brain Female	brain
4	chr15:59468200-59528600	Weak transcription	Stomach Mucosa	stomach
5	chr15:59468600-59521400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr15:59468800-59490800	Strong transcription	Duodenum Mucosa	Duodenum
7	chr15:59468800-59492600	Strong transcription	Fetal Intestine Large	intestine
8	chr15:59470800-59485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:59474400-59484600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:59475200-59486800	Weak transcription	Pancreas	Pancrea
11	chr15:59475200-59503200	Strong transcription	Liver	Liver
12	chr15:59475400-59485200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:59475800-59498200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:59475800-59517800	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:59476000-59488000	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:59476200-59490600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr15:59476800-59486400	Weak transcription	Right Ventricle	heart
18	chr15:59477000-59498000	Strong transcription	GM12878-XiMat	blood
19	chr15:59477600-59485400	Weak transcription	Small Intestine	intestine
20	chr15:59477800-59486800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:59478800-59486800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:59479400-59487800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:59479400-59488200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:59479600-59488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:59480200-59492400	Weak transcription	Fetal Heart	heart
26	chr15:59480200-59499200	Weak transcription	Fetal Lung	lung
27	chr15:59480200-59507200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:59480400-59484200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:59480400-59484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr15:59480400-59486800	Weak transcription	Psoas Muscle	Psoas
31	chr15:59480600-59484600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:59480600-59485000	Weak transcription	Ovary	ovary
33	chr15:59480600-59485200	Weak transcription	Brain Anterior Caudate	brain
34	chr15:59480600-59496400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:59480600-59507600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr15:59481000-59485000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr15:59481000-59487800	Strong transcription	Primary B cells from cord blood	blood
38	chr15:59481000-59492000	Strong transcription	Fetal Intestine Small	intestine
39	chr15:59481400-59487600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:59481400-59496000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:59481600-59485000	Enhancers	HSMMtube	muscle
42	chr15:59481600-59488600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:59481800-59487800	Strong transcription	Fetal Muscle Trunk	muscle
44	chr15:59481800-59487800	Strong transcription	Left Ventricle	heart
45	chr15:59482000-59487600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:59482000-59487800	Strong transcription	Fetal Muscle Leg	muscle
47	chr15:59482200-59485800	Strong transcription	Rectal Smooth Muscle	rectum
48	chr15:59482200-59487800	Strong transcription	Spleen	Spleen
49	chr15:59482200-59488000	Strong transcription	Gastric	stomach
50	chr15:59482400-59487800	Strong transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links