Variant report

Variant	rs4128469
Chromosome Location	chr8:125479475-125479476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:125463054..125465256-chr8:125476799..125479524,2	K562	blood:
2	chr8:125475979..125479688-chr8:125483655..125487950,7	K562	blood:
3	chr8:125461213..125466499-chr8:125476927..125481847,6	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TATDN1-1	chr8:125474740-125479899	XLOC_007206
2	lnc-TATDN1-1	chr8:125474726-125479899	ENSG00000245149
3	lnc-TATDN1-1	chr8:125479460-125479899	NONHSAT128584
4	lnc-TATDN1-1	chr8:125474738-125479899	NR_108047

No data

Variant related genes	Relation type
ENSG00000170881	Chromatin interaction
ENSG00000183665	Chromatin interaction
ENSG00000245149	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10956184	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10956185	0.88[CEU][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11986208	0.88[JPT][hapmap]
rs12542260	0.88[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12548836	0.88[CEU][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs16899649	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs16899653	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs3829038	0.82[JPT][hapmap];0.91[YRI][hapmap]
rs4132855	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4301437	0.88[JPT][hapmap]
rs4512366	0.88[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]
rs4551335	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4870898	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4870899	0.81[AFR][1000 genomes]
rs5004281	0.88[CEU][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62527880	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62527881	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62527882	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62527883	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62527884	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62527886	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62527901	0.81[EUR][1000 genomes]
rs62527908	0.81[EUR][1000 genomes]
rs62527910	0.81[EUR][1000 genomes]
rs6987213	0.88[CEU][hapmap]
rs72713049	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812363	0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7826104	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7830325	0.88[CEU][hapmap]
rs7834203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7836802	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7845008	0.88[CEU][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1034768	chr8:125323011-125481733	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv891430	chr8:125431030-125485027	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1017848	chr8:125432689-125489052	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv891431	chr8:125437811-125485027	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv891432	chr8:125438093-125485027	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv891433	chr8:125438093-125498547	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4128469	SAMSN1	trans	lymphoblastoid	seeQTL
rs4128469	ZHX2	cis	cerebellum	SCAN
rs4128469	HAS2	cis	parietal	SCAN
rs4128469	ZHX2	cis	parietal	SCAN
rs4128469	TRIB1	cis	parietal	SCAN
rs4128469	TRMT12	cis	multi-tissue	Pritchard
rs4128469	TRMT12	cis	Whole Blood	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125463800-125483800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr8:125464000-125484800	Weak transcription	Aorta	Aorta
3	chr8:125464000-125485000	Weak transcription	Fetal Kidney	kidney
4	chr8:125464400-125479600	Weak transcription	Fetal Intestine Large	intestine
5	chr8:125464600-125483200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr8:125464600-125484600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr8:125464600-125485200	Weak transcription	Colonic Mucosa	Colon
8	chr8:125464600-125485800	Weak transcription	Esophagus	oesophagus
9	chr8:125464600-125486000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:125464800-125484600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr8:125464800-125484800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr8:125464800-125485400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr8:125465000-125484400	Weak transcription	NHLF	lung
14	chr8:125465000-125485400	Weak transcription	Gastric	stomach
15	chr8:125465200-125483000	Weak transcription	Fetal Brain Male	brain
16	chr8:125465200-125483200	Weak transcription	Fetal Lung	lung
17	chr8:125465600-125482800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:125465600-125484200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr8:125465600-125484600	Weak transcription	HMEC	breast
20	chr8:125465600-125485200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr8:125466000-125485400	Weak transcription	Lung	lung
22	chr8:125466200-125484600	Weak transcription	Right Ventricle	heart
23	chr8:125466400-125482800	Weak transcription	NHDF-Ad	bronchial
24	chr8:125466400-125483000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr8:125466400-125483000	Weak transcription	Brain Anterior Caudate	brain
26	chr8:125466400-125483200	Weak transcription	Spleen	Spleen
27	chr8:125466400-125484000	Weak transcription	Ovary	ovary
28	chr8:125466400-125484600	Weak transcription	A549	lung
29	chr8:125466400-125484800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr8:125466400-125484800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:125466600-125484000	Weak transcription	Fetal Muscle Leg	muscle
32	chr8:125466800-125482800	Weak transcription	Colon Smooth Muscle	Colon
33	chr8:125467200-125484400	Weak transcription	Thymus	Thymus
34	chr8:125467200-125484600	Weak transcription	Brain Angular Gyrus	brain
35	chr8:125467200-125484600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr8:125467200-125485400	Weak transcription	Left Ventricle	heart
37	chr8:125468000-125483000	Weak transcription	Hela-S3	cervix
38	chr8:125468200-125482800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr8:125468400-125483800	Weak transcription	NHEK	skin
40	chr8:125468400-125485200	Weak transcription	Brain Substantia Nigra	brain
41	chr8:125469000-125482800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr8:125469200-125482800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr8:125469800-125484000	Weak transcription	Placenta	Placenta
44	chr8:125472400-125482800	Weak transcription	GM12878-XiMat	blood
45	chr8:125473400-125485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr8:125473600-125484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr8:125474400-125479600	Strong transcription	Fetal Brain Female	brain
48	chr8:125474400-125479800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:125474600-125480000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr8:125474600-125481000	Strong transcription	Primary B cells from cord blood	blood

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