Variant report

Variant	rs1446674
Chromosome Location	chr2:179973325-179973326
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10174774	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap]
rs10186198	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10188759	0.82[TSI][hapmap]
rs10192426	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10205390	0.83[ASW][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs10209887	0.82[TSI][hapmap]
rs1158872	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11884516	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap]
rs11894870	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11898291	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs12622075	0.82[TSI][hapmap]
rs12997314	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs13026497	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap]
rs13382185	0.82[TSI][hapmap]
rs13418701	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap]
rs1374378	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1374379	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1979053	0.88[EUR][1000 genomes]
rs2008989	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2008999	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289992	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2847	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs340331	0.82[GIH][hapmap]
rs4585064	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6433757	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433760	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6433761	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6433764	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6707081	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs6736098	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6742744	0.82[YRI][hapmap]
rs6743405	0.83[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757681	0.88[YRI][hapmap]
rs7579536	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7585600	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs7608882	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs873023	0.88[YRI][hapmap]
rs9288022	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1446674	SESTD1	cis	cerebellum	SCAN
rs1446674	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs1446674	SESTD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179961600-179974000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:179966400-179975600	Weak transcription	Aorta	Aorta
3	chr2:179967200-179976800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:179967800-179980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
6	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
7	chr2:179969400-179980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
10	chr2:179970400-179977000	Weak transcription	Lung	lung
11	chr2:179970600-179973800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:179970800-179973400	Enhancers	HUVEC	blood vessel
13	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
14	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:179971000-179974000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:179971200-179973400	Genic enhancers	Dnd41	blood
17	chr2:179971200-179973400	Genic enhancers	HepG2	liver
18	chr2:179971200-179977600	Strong transcription	Fetal Lung	lung
19	chr2:179971200-179977800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:179971400-179973400	Enhancers	NHLF	lung
21	chr2:179971400-179979200	Weak transcription	Ovary	ovary
22	chr2:179971600-179974000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:179971600-179974200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:179971600-179974200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:179971600-179977000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:179971600-179977000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:179971600-179977000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr2:179971600-179979400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:179971800-179978400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:179972000-179973400	Enhancers	A549	lung
33	chr2:179972000-179973800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:179972000-179974000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:179972000-179976800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:179972200-179974200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:179972200-179982400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:179972400-179973400	Genic enhancers	HSMM	muscle
41	chr2:179972400-179973400	Genic enhancers	Osteobl	bone
42	chr2:179972400-179974000	Strong transcription	Fetal Brain Female	brain
43	chr2:179972400-179975800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:179972400-179977600	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr2:179972400-179979800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:179972400-179982200	Strong transcription	Liver	Liver
47	chr2:179972400-179985400	Strong transcription	Stomach Smooth Muscle	stomach
48	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr2:179972600-179973400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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