Variant report

Variant	rs7558968
Chromosome Location	chr2:53949945-53949946
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	chr2:53949409..53951180-chr2:53951221..53954133,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10490468	0.82[ASN][1000 genomes]
rs11897282	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11901698	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13408029	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045176	0.86[ASN][1000 genomes]
rs17520505	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17521008	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2008082	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2302797	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2542572	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2542578	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2542580	0.86[EUR][1000 genomes]
rs2542581	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2543629	0.82[EUR][1000 genomes]
rs2692523	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35772199	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3770394	0.88[ASN][1000 genomes]
rs3770395	0.88[ASN][1000 genomes]
rs3770397	0.86[ASN][1000 genomes]
rs3770399	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4116709	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56214822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56228834	0.86[ASN][1000 genomes]
rs62137565	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62137566	0.81[AMR][1000 genomes]
rs62137573	0.87[ASN][1000 genomes]
rs62137602	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137606	0.86[ASN][1000 genomes]
rs6730006	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs719127	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72901256	0.90[ASN][1000 genomes]
rs7583622	0.81[AMR][1000 genomes]
rs7600817	0.88[ASN][1000 genomes]
rs805435	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv1844655	chr2:53929855-53972693	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
3	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
6	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
7	chr2:53927600-53960200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:53936600-53968400	Weak transcription	Pancreas	Pancrea
9	chr2:53936600-53978600	Weak transcription	Hela-S3	cervix
10	chr2:53936800-53985400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:53937000-53983800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:53937200-53954000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:53937200-53955800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:53937200-53961400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:53937200-53964400	Weak transcription	Aorta	Aorta
17	chr2:53937200-53966800	Weak transcription	Gastric	stomach
18	chr2:53937200-53978600	Weak transcription	NH-A	brain
19	chr2:53937200-53983600	Weak transcription	Right Ventricle	heart
20	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:53937400-53954000	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:53937400-53964000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:53937400-53979600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:53937600-53961600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:53937800-53957000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:53938000-53956400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:53938000-53961400	Weak transcription	NHEK	skin
30	chr2:53938000-53974800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:53938000-53974800	Weak transcription	Placenta	Placenta
32	chr2:53938200-53967000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:53938200-53975200	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:53938400-53963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:53938400-53969400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:53938400-53969600	Weak transcription	Esophagus	oesophagus
37	chr2:53938400-53975000	Weak transcription	Fetal Kidney	kidney
38	chr2:53938400-53982800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:53938400-53983400	Weak transcription	HSMMtube	muscle
40	chr2:53938400-53992400	Weak transcription	K562	blood
41	chr2:53938600-53954400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:53938600-53955200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:53938600-53961000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:53938600-53972000	Weak transcription	HSMM	muscle
45	chr2:53939000-53954000	Weak transcription	Lung	lung
46	chr2:53939000-53954000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:53940600-53957400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:53941000-53952200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:53941600-53956400	Weak transcription	GM12878-XiMat	blood
50	chr2:53941800-53956400	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links