Variant report

Variant	rs7431968
Chromosome Location	chr3:88202045-88202046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1006896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10858	0.87[ASN][1000 genomes]
rs11925988	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493327	1.00[JPT][hapmap]
rs13074910	1.00[CEU][hapmap]
rs13317202	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2735559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4858934	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858939	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858940	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859003	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55883959	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs55928667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932154	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211058	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246133	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419868	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419869	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6551276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551295	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73132512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73132546	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146085	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146095	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73146099	0.87[ASN][1000 genomes]
rs73148006	0.80[ASN][1000 genomes]
rs7430022	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432826	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432838	1.00[JPT][hapmap]
rs7610494	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620576	0.89[EUR][1000 genomes]
rs7620830	1.00[JPT][hapmap]
rs7624215	0.91[EUR][1000 genomes]
rs7650068	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284814	0.87[EUR][1000 genomes]
rs9826925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7431968	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs7431968	CGGBP1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88199600-88203400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:88199600-88203800	Weak transcription	Spleen	Spleen
3	chr3:88199800-88202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:88199800-88203200	Weak transcription	Lung	lung
5	chr3:88199800-88204000	Weak transcription	Gastric	stomach
6	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
7	chr3:88200000-88202400	Weak transcription	Left Ventricle	heart
8	chr3:88200000-88202400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:88200000-88202600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:88200000-88203800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:88200200-88202400	Weak transcription	Small Intestine	intestine
12	chr3:88200200-88202600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:88200200-88205600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:88200400-88202600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:88200400-88203400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr3:88200800-88202400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:88200800-88202400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:88200800-88202400	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:88200800-88202600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:88200800-88202600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr3:88200800-88202600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:88200800-88202800	Weak transcription	Fetal Stomach	stomach
23	chr3:88200800-88203400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:88200800-88204000	Weak transcription	Fetal Intestine Small	intestine
25	chr3:88200800-88204000	Weak transcription	Ovary	ovary
26	chr3:88200800-88204800	Weak transcription	Right Ventricle	heart
27	chr3:88200800-88205200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:88200800-88209400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:88200800-88214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
31	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
32	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
33	chr3:88201000-88202200	Enhancers	Primary B cells from cord blood	blood
34	chr3:88201000-88202400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:88201000-88202400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:88201000-88203000	Weak transcription	Fetal Kidney	kidney
37	chr3:88201000-88203600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:88201000-88203600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:88201000-88205200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:88201200-88202200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:88201200-88202200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:88201200-88202200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:88201200-88202200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:88201200-88202200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:88201200-88202200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:88201200-88202200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:88201200-88202200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:88201200-88202200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr3:88201200-88202200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:88201200-88202200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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