Variant report

Variant	rs55950446
Chromosome Location	chr3:100013101-100013102
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100012557..100015555-chr3:100016253..100017755,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1060452	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11918291	0.90[EUR][1000 genomes]
rs11920015	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11923373	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11924911	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486660	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486865	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12490043	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12490140	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12492610	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12493917	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17335566	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17335614	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2171205	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs277657	0.82[EUR][1000 genomes]
rs4928116	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4928117	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4928161	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4928166	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928170	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56181320	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56311459	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57271189	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62281663	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
2	chr3:99980600-100053200	Weak transcription	Gastric	stomach
3	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
4	chr3:99986600-100024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:99988800-100013800	Weak transcription	Fetal Brain Male	brain
6	chr3:99989000-100025000	Weak transcription	Fetal Brain Female	brain
7	chr3:99990600-100030600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:99990800-100021400	Weak transcription	Psoas Muscle	Psoas
9	chr3:99992400-100017600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:99994200-100014200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
12	chr3:99995400-100019000	Weak transcription	Colonic Mucosa	Colon
13	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
15	chr3:99996400-100025600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:99996800-100016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:99997200-100017800	Weak transcription	Brain Angular Gyrus	brain
18	chr3:99997600-100017000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:99997800-100031800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:99998000-100013600	Weak transcription	Fetal Kidney	kidney
21	chr3:99998200-100013400	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:99998200-100016200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:99998400-100028000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:99998600-100015400	Strong transcription	Osteobl	bone
25	chr3:99998600-100026400	Strong transcription	HSMM	muscle
26	chr3:99998600-100033800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:99998800-100019800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:99998800-100021800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:99998800-100026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:100000800-100015800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:100001000-100014200	Weak transcription	Stomach Mucosa	stomach
32	chr3:100001600-100014000	Weak transcription	GM12878-XiMat	blood
33	chr3:100001800-100014200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:100002200-100013600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:100002400-100018400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:100003400-100015000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:100005200-100013600	Weak transcription	HepG2	liver
38	chr3:100005200-100021600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:100005800-100015000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:100006000-100018000	Weak transcription	Ovary	ovary
41	chr3:100006000-100019800	Weak transcription	Hela-S3	cervix
42	chr3:100006800-100016400	Weak transcription	NHEK	skin
43	chr3:100007000-100018000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:100007000-100045000	Weak transcription	Lung	lung
45	chr3:100007800-100035800	Weak transcription	A549	lung
46	chr3:100008000-100015800	Strong transcription	NHDF-Ad	bronchial
47	chr3:100008000-100019600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:100008200-100015400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:100008200-100022200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:100008400-100013800	Weak transcription	NHLF	lung

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