Variant report

Variant	rs1662946
Chromosome Location	chr2:30672580-30672581
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30659383..30661784-chr2:30671941..30674589,2	K562	blood:
2	chr2:30659383..30660987-chr2:30671941..30673568,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10167083	0.92[AMR][1000 genomes]
rs10183928	0.85[AMR][1000 genomes]
rs10865520	0.80[EUR][1000 genomes]
rs1096109	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11127278	0.82[AMR][1000 genomes]
rs12053428	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12468064	0.81[AMR][1000 genomes]
rs1252631	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1252640	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1252651	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869423	0.86[AMR][1000 genomes]
rs1975555	0.89[AMR][1000 genomes]
rs2123753	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2177698	0.81[AMR][1000 genomes]
rs2593440	0.86[AMR][1000 genomes]
rs2593442	0.83[AMR][1000 genomes]
rs2593443	0.89[AMR][1000 genomes]
rs2593448	0.89[AMR][1000 genomes]
rs2593455	0.85[AMR][1000 genomes]
rs2593474	0.89[AMR][1000 genomes]
rs2602806	0.86[AMR][1000 genomes]
rs2602807	0.86[AMR][1000 genomes]
rs2602808	0.83[AMR][1000 genomes]
rs2609924	0.89[AMR][1000 genomes]
rs2609925	0.89[AMR][1000 genomes]
rs2609926	0.83[AMR][1000 genomes]
rs2609943	0.89[AMR][1000 genomes]
rs3862977	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6731031	0.81[AMR][1000 genomes]
rs7566983	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7591110	0.81[AMR][1000 genomes]
rs829563	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829564	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829565	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829581	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829616	0.80[EUR][1000 genomes]
rs829617	0.80[EUR][1000 genomes]
rs829630	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs829632	0.81[EUR][1000 genomes]
rs829635	0.80[EUR][1000 genomes]
rs829637	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs829639	0.98[EUR][1000 genomes]
rs829653	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829664	0.81[EUR][1000 genomes]
rs829681	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829684	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829694	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829695	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829696	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829699	0.82[ASN][1000 genomes]
rs829700	0.82[ASN][1000 genomes]
rs860487	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs866680	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs895665	0.86[AMR][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

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671000-30674200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:30671000-30675600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:30671000-30675600	Weak transcription	Psoas Muscle	Psoas
4	chr2:30671000-30677400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:30671000-30678200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:30671000-30678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:30671000-30679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:30671000-30682000	Weak transcription	Aorta	Aorta
9	chr2:30671000-30685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr2:30671200-30672600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr2:30671200-30678400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:30671200-30681200	Weak transcription	Right Atrium	heart
13	chr2:30671200-30688200	Weak transcription	HSMM	muscle
14	chr2:30671400-30673000	Enhancers	Liver	Liver
15	chr2:30671400-30673400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:30671400-30673800	Enhancers	Fetal Intestine Large	intestine
17	chr2:30671600-30672600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:30671600-30673000	Weak transcription	Left Ventricle	heart
19	chr2:30671600-30673800	Enhancers	Fetal Intestine Small	intestine
20	chr2:30671600-30674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:30671600-30674400	Weak transcription	NHEK	skin
22	chr2:30671600-30675600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:30671600-30675600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:30671600-30676400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:30671600-30676800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:30671600-30678400	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:30671600-30678800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:30671600-30679000	Weak transcription	Lung	lung
29	chr2:30671600-30682000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:30671600-30682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:30671600-30683800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr2:30671600-30685600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:30671600-30688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:30671600-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:30671800-30672800	Weak transcription	Stomach Mucosa	stomach
39	chr2:30671800-30673000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:30671800-30673600	Enhancers	HepG2	liver
41	chr2:30671800-30673800	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr2:30671800-30675400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:30671800-30675600	Weak transcription	Fetal Brain Female	brain
44	chr2:30671800-30677400	Weak transcription	Small Intestine	intestine
45	chr2:30671800-30679600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:30671800-30679600	Weak transcription	Fetal Kidney	kidney
47	chr2:30671800-30681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:30672000-30672800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:30672000-30672800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:30672000-30672800	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links