Variant report

Variant	rs5028414
Chromosome Location	chr3:67562990-67562991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11919650	0.83[EUR][1000 genomes]
rs11919747	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11923127	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11927204	0.83[EUR][1000 genomes]
rs12488930	0.83[EUR][1000 genomes]
rs12489287	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12495506	0.94[ASN][1000 genomes]
rs12636825	0.85[EUR][1000 genomes]
rs17046528	0.83[EUR][1000 genomes]
rs17046546	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17046548	0.90[ASN][1000 genomes]
rs4371532	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856869	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856870	0.94[ASN][1000 genomes]
rs4856872	0.81[EUR][1000 genomes]
rs4856873	0.81[EUR][1000 genomes]
rs4856874	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4856875	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56246741	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56361934	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58093651	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61386974	0.83[EUR][1000 genomes]
rs6548615	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6784255	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72923195	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72924913	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7623441	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3486435	chr3:67561062-67564760	Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv3486433	chr3:67561512-67564610	Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3461975	chr3:67562052-67563719	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
11	esv3461977	chr3:67562107-67563706	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
12	esv3486432	chr3:67562114-67563699	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
13	esv3461976	chr3:67562134-67563662	Strong transcription Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
14	esv3486431	chr3:67562134-67563751	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
15	esv3486434	chr3:67562137-67563669	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
16	esv3461978	chr3:67562164-67563693	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
17	esv21281	chr3:67562171-67563622	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
18	esv3461979	chr3:67562195-67563619	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
19	esv3486436	chr3:67562203-67563621	Weak transcription Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
3	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
4	chr3:67511800-67565000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:67513200-67564800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:67513400-67567800	Weak transcription	NHLF	lung
7	chr3:67521600-67580400	Weak transcription	Stomach Mucosa	stomach
8	chr3:67524200-67567000	Weak transcription	Placenta	Placenta
9	chr3:67526800-67583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:67528200-67564400	Weak transcription	Fetal Lung	lung
11	chr3:67528200-67564800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:67531400-67576200	Weak transcription	HMEC	breast
13	chr3:67533200-67577000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:67533400-67577600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:67534400-67576400	Weak transcription	Aorta	Aorta
16	chr3:67534600-67566200	Weak transcription	Gastric	stomach
17	chr3:67534800-67566200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:67535000-67578800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:67537400-67579600	Weak transcription	Small Intestine	intestine
20	chr3:67537600-67566800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:67540800-67564400	Weak transcription	Fetal Kidney	kidney
22	chr3:67541400-67582000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:67542400-67564800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:67542400-67566400	Weak transcription	NH-A	brain
25	chr3:67543200-67566000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:67544200-67580200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr3:67544400-67567200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr3:67544800-67577600	Weak transcription	Thymus	Thymus
29	chr3:67545400-67564400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:67546400-67565000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:67546600-67563800	Weak transcription	Dnd41	blood
32	chr3:67546600-67564000	Weak transcription	HSMM	muscle
33	chr3:67546600-67564600	Weak transcription	A549	lung
34	chr3:67546600-67564800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr3:67546600-67566400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:67546800-67565000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:67547000-67564200	Weak transcription	Colonic Mucosa	Colon
38	chr3:67552000-67566800	Weak transcription	HepG2	liver
39	chr3:67552200-67566200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:67553800-67579600	Weak transcription	Hela-S3	cervix
41	chr3:67554600-67565000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:67554600-67577800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:67555200-67563600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:67555400-67566200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:67555800-67566200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:67555800-67567800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:67555800-67579600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:67556000-67566200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:67557400-67583200	Weak transcription	K562	blood
50	chr3:67558400-67571400	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links