Variant report

Variant	rs334699
Chromosome Location	chr1:61620496-61620497
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:61599982..61604281-chr1:61617367..61621050,4	K562	blood:
2	chr1:61605231..61608148-chr1:61617822..61620797,4	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12064543	0.93[EUR][1000 genomes]
rs12070080	0.93[EUR][1000 genomes]
rs17121598	0.93[EUR][1000 genomes]
rs2807991	0.93[EUR][1000 genomes]
rs334698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334701	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.97[AFR][1000 genomes]
rs334702	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs334703	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334708	0.82[CEU][hapmap]
rs334709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334710	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs334712	0.82[CEU][hapmap]
rs334713	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334716	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs334718	0.84[EUR][1000 genomes]
rs334719	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs334721	0.90[EUR][1000 genomes]
rs334723	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs334725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334727	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334729	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs334730	0.93[EUR][1000 genomes]
rs334731	0.93[EUR][1000 genomes]
rs334733	0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs334734	0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs334737	0.93[EUR][1000 genomes]
rs334739	0.93[EUR][1000 genomes]
rs3748543	0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs395936	0.90[ASW][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs406412	0.90[ASW][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes]
rs440611	0.93[EUR][1000 genomes]
rs4546954	0.93[EUR][1000 genomes]
rs4915586	0.93[EUR][1000 genomes]
rs6587912	0.93[EUR][1000 genomes]
rs694151	0.85[YRI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs694161	0.85[YRI][hapmap];0.90[EUR][1000 genomes];0.82[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	nsv1008634	chr1:61613785-61671468	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid hormone levels	23408906	GWAS catalog

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:61606000-61649000	Weak transcription	Spleen	Spleen
2	chr1:61607600-61622200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:61607800-61622600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:61609600-61622800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:61610000-61621800	Weak transcription	Fetal Brain Male	brain
6	chr1:61610000-61623400	Weak transcription	Fetal Brain Female	brain
7	chr1:61610200-61622200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:61610200-61623200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:61612000-61635800	Weak transcription	Lung	lung
10	chr1:61612800-61626200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:61613800-61620600	Enhancers	Brain Hippocampus Middle	brain
12	chr1:61614800-61622000	Weak transcription	Ovary	ovary
13	chr1:61615200-61620600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:61615200-61621000	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:61615400-61635000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:61615400-61635600	Weak transcription	Hela-S3	cervix
17	chr1:61615600-61620600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:61615600-61622600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:61615600-61622600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:61615800-61621600	Weak transcription	Right Ventricle	heart
21	chr1:61615800-61621800	Weak transcription	K562	blood
22	chr1:61615800-61622400	Weak transcription	NHEK	skin
23	chr1:61616000-61622000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:61616000-61628000	Weak transcription	Gastric	stomach
25	chr1:61616800-61622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:61616800-61623200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:61617000-61627800	Weak transcription	Esophagus	oesophagus
28	chr1:61617200-61620600	Enhancers	Fetal Stomach	stomach
29	chr1:61617200-61620800	Enhancers	Fetal Intestine Large	intestine
30	chr1:61618000-61622600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:61618000-61622600	Weak transcription	Brain Germinal Matrix	brain
32	chr1:61618000-61628000	Weak transcription	Pancreas	Pancrea
33	chr1:61618200-61622600	Weak transcription	Left Ventricle	heart
34	chr1:61618600-61623400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:61618800-61621600	Weak transcription	Psoas Muscle	Psoas
36	chr1:61618800-61622200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:61618800-61622200	Weak transcription	Adipose Nuclei	Adipose
38	chr1:61618800-61622200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:61618800-61622400	Weak transcription	Fetal Muscle Leg	muscle
40	chr1:61618800-61622600	Weak transcription	Right Atrium	heart
41	chr1:61618800-61623000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:61618800-61623000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:61619000-61622000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:61619000-61622200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:61619000-61622400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:61619200-61622000	Weak transcription	Fetal Kidney	kidney
47	chr1:61619200-61622400	Weak transcription	A549	lung
48	chr1:61619200-61649000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:61619400-61622000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:61619400-61622200	Weak transcription	Brain Angular Gyrus	brain

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