Variant report

Variant	rs4975139
Chromosome Location	chr4:79455733-79455734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10025220	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11098224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098225	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098228	0.86[CHB][hapmap]
rs11936220	0.92[CHB][hapmap]
rs11940309	0.86[CHB][hapmap]
rs12639818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12648204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13121431	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390744	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390746	0.88[EUR][1000 genomes]
rs1496594	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496595	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1496596	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17003337	0.84[CHB][hapmap]
rs28391466	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28434623	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28514647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867445	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749485	0.86[CHB][hapmap]
rs3811747	0.86[CHB][hapmap]
rs4610364	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4975070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975134	0.82[EUR][1000 genomes]
rs56212709	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61284375	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533756	0.85[EUR][1000 genomes]
rs7664814	0.84[EUR][1000 genomes]
rs7677541	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4975139	GDI2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79363800-79464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:79378600-79455800	Weak transcription	Right Ventricle	heart
3	chr4:79385000-79467400	Weak transcription	Fetal Brain Male	brain
4	chr4:79393800-79467200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:79401000-79467200	Weak transcription	Psoas Muscle	Psoas
6	chr4:79410200-79461800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:79428200-79466200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:79428600-79459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:79430200-79456000	Weak transcription	Aorta	Aorta
10	chr4:79430200-79456000	Weak transcription	Pancreas	Pancrea
11	chr4:79435600-79463000	Weak transcription	Fetal Heart	heart
12	chr4:79435600-79467200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:79440600-79465800	Weak transcription	Lung	lung
14	chr4:79440600-79467200	Weak transcription	Left Ventricle	heart
15	chr4:79440800-79456200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:79442400-79465600	Weak transcription	Fetal Stomach	stomach
17	chr4:79444800-79472400	Weak transcription	Right Atrium	heart
18	chr4:79446600-79456000	Weak transcription	Fetal Intestine Large	intestine
19	chr4:79451400-79462800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:79451600-79461600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:79451800-79463400	Weak transcription	NHDF-Ad	bronchial
22	chr4:79451800-79463800	Weak transcription	NH-A	brain
23	chr4:79452000-79461600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:79453400-79464200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:79453400-79467200	Weak transcription	Placenta	Placenta
26	chr4:79453600-79457000	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr4:79454200-79457600	Enhancers	HMEC	breast
28	chr4:79454400-79456800	Enhancers	NHEK	skin
29	chr4:79454600-79456800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:79454600-79456800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:79454600-79458600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:79454600-79463800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr4:79454800-79456000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:79454800-79456000	Enhancers	Brain Anterior Caudate	brain
35	chr4:79454800-79456600	Weak transcription	Primary B cells from cord blood	blood
36	chr4:79454800-79463600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:79455000-79456000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:79455000-79456000	Enhancers	HSMMtube	muscle
39	chr4:79455000-79456600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:79455000-79463400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr4:79455200-79456200	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr4:79455200-79456200	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr4:79455200-79456200	Enhancers	Brain Hippocampus Middle	brain
44	chr4:79455200-79456400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:79455200-79460400	Weak transcription	Esophagus	oesophagus
46	chr4:79455400-79455800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:79455400-79456000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:79455400-79456200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr4:79455400-79463200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr4:79455400-79464400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links