Variant report

Variant	rs1662949
Chromosome Location	chr2:30671843-30671844
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30454671..30456447-chr2:30669328..30672295,2	K562	blood:

Variant related genes	Relation type
ENSG00000213626	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11686191	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11892635	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1252639	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252641	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252643	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1252647	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1614348	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1615605	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1662941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1662958	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1723156	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1723167	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1723170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723175	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2692041	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28538173	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35418935	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952124	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952148	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72853154	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7562645	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs829562	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829570	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829571	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829573	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829576	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829577	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829579	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829584	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829623	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829636	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829638	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs829645	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829647	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829648	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829649	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829650	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829651	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs829658	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829686	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829687	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829689	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829690	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs829693	0.86[EUR][1000 genomes];0.87[ASN][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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1662949	LYCAT	cis	multi-tissue	Pritchard
rs1662949	LYCAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30669400-30672000	Active TSS	Right Ventricle	heart
2	chr2:30670600-30672000	Flanking Active TSS	Dnd41	blood
3	chr2:30670600-30672000	Flanking Active TSS	K562	blood
4	chr2:30670800-30672000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr2:30671000-30672000	Enhancers	Primary B cells from peripheral blood	blood
6	chr2:30671000-30672000	Enhancers	Fetal Lung	lung
7	chr2:30671000-30672000	Flanking Active TSS	A549	lung
8	chr2:30671000-30674200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:30671000-30675600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:30671000-30675600	Weak transcription	Psoas Muscle	Psoas
11	chr2:30671000-30677400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:30671000-30678200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:30671000-30678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:30671000-30679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:30671000-30682000	Weak transcription	Aorta	Aorta
16	chr2:30671000-30685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:30671200-30672000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr2:30671200-30672000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:30671200-30672000	Enhancers	Ovary	ovary
20	chr2:30671200-30672000	Enhancers	Thymus	Thymus
21	chr2:30671200-30672000	Active TSS	NHLF	lung
22	chr2:30671200-30672600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:30671200-30678400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:30671200-30681200	Weak transcription	Right Atrium	heart
25	chr2:30671200-30688200	Weak transcription	HSMM	muscle
26	chr2:30671400-30672000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr2:30671400-30672000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:30671400-30672000	Enhancers	HMEC	breast
29	chr2:30671400-30672000	Enhancers	HUVEC	blood vessel
30	chr2:30671400-30673000	Enhancers	Liver	Liver
31	chr2:30671400-30673400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:30671400-30673800	Enhancers	Fetal Intestine Large	intestine
33	chr2:30671600-30672000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:30671600-30672000	Enhancers	Primary B cells from cord blood	blood
35	chr2:30671600-30672000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:30671600-30672000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:30671600-30672000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr2:30671600-30672000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:30671600-30672000	Enhancers	Fetal Thymus	thymus
40	chr2:30671600-30672000	Enhancers	Stomach Smooth Muscle	stomach
41	chr2:30671600-30672000	Enhancers	Hela-S3	cervix
42	chr2:30671600-30672400	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:30671600-30672400	Weak transcription	Gastric	stomach
44	chr2:30671600-30672400	Weak transcription	Pancreas	Pancrea
45	chr2:30671600-30672600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:30671600-30673000	Weak transcription	Left Ventricle	heart
47	chr2:30671600-30673800	Enhancers	Fetal Intestine Small	intestine
48	chr2:30671600-30674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:30671600-30674400	Weak transcription	NHEK	skin
50	chr2:30671600-30675600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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