Variant report

Variant	rs3816345
Chromosome Location	chr2:179974885-179974886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1048026	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10497534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10497535	0.87[YRI][hapmap]
rs11892241	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11897308	1.00[ASW][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs11900884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11901408	0.92[YRI][hapmap]
rs11901421	1.00[ASW][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs11903685	0.91[YRI][hapmap]
rs12105478	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs1490997	1.00[ASW][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs16866635	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs16866636	0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs16866665	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16866667	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs16866673	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17363449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17363603	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17453976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17454192	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17454458	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs1838872	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2008215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044477	0.93[AFR][1000 genomes]
rs2305170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4101465	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4499457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60072979	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61179885	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433758	0.88[AFR][1000 genomes]
rs6433759	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433762	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs6433765	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6433766	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707001	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs6710100	1.00[ASW][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs6723850	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs6725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6728401	0.92[YRI][hapmap]
rs6752298	0.81[AFR][1000 genomes]
rs7566810	0.88[ASW][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7598995	0.80[AFR][1000 genomes]
rs879539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930620	0.96[YRI][hapmap];0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179966400-179975600	Weak transcription	Aorta	Aorta
2	chr2:179967200-179976800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:179967800-179980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
5	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
6	chr2:179969400-179980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
9	chr2:179970400-179977000	Weak transcription	Lung	lung
10	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
11	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:179971200-179977600	Strong transcription	Fetal Lung	lung
13	chr2:179971200-179977800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:179971400-179979200	Weak transcription	Ovary	ovary
15	chr2:179971600-179977000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:179971600-179977000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:179971600-179977000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:179971600-179979400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:179971800-179978400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:179972000-179976800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:179972200-179982400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:179972400-179975800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:179972400-179977600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:179972400-179979800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:179972400-179982200	Strong transcription	Liver	Liver
30	chr2:179972400-179985400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:179972600-179975000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:179972600-179976800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:179972600-179977000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr2:179972600-179977600	Strong transcription	Brain Germinal Matrix	brain
37	chr2:179972600-179979600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:179972600-179979800	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:179972600-179985200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:179972600-179985200	Weak transcription	Fetal Heart	heart
41	chr2:179972600-180001800	Weak transcription	NHEK	skin
42	chr2:179972800-179975800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:179972800-179977600	Strong transcription	Fetal Muscle Leg	muscle
44	chr2:179972800-179979400	Weak transcription	Thymus	Thymus
45	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:179973000-179976600	Weak transcription	HSMMtube	muscle
48	chr2:179973000-179977000	Weak transcription	NH-A	brain
49	chr2:179973000-179982400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr2:179973000-179982600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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