Variant report

Variant	rs3109952
Chromosome Location	chr4:107263476-107263477
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	chr4:107243946..107245943-chr4:107262663..107264283,2	K562	blood:
2	chr4:107235907..107237713-chr4:107263142..107264645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145348	Chromatin interaction
ENSG00000164022	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10004034	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10017707	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10025668	0.80[ASN][1000 genomes]
rs10516530	0.93[ASN][1000 genomes]
rs10516531	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097923	0.95[ASN][1000 genomes]
rs1134648	1.00[ASN][1000 genomes]
rs11938792	0.95[ASN][1000 genomes]
rs12512475	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17036581	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2691805	1.00[ASN][1000 genomes]
rs2691806	1.00[ASN][1000 genomes]
rs2728176	1.00[ASN][1000 genomes]
rs2728177	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418378	0.80[ASN][1000 genomes]
rs2949626	0.99[ASN][1000 genomes]
rs2949649	0.94[ASN][1000 genomes]
rs2949651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3018057	0.93[ASN][1000 genomes]
rs3018059	0.99[ASN][1000 genomes]
rs3018067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3109950	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3109951	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3109954	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109956	1.00[ASN][1000 genomes]
rs3109959	0.98[ASN][1000 genomes]
rs3113246	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3113251	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133167	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3133172	1.00[ASN][1000 genomes]
rs3133173	0.96[ASN][1000 genomes]
rs34305991	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34923623	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4415033	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4441824	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4560491	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4582218	0.94[ASN][1000 genomes]
rs57983950	0.94[ASN][1000 genomes]
rs6533241	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533244	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6848855	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7442226	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7669347	0.81[ASN][1000 genomes]
rs7677394	0.94[ASN][1000 genomes]
rs7680756	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7694217	0.95[ASN][1000 genomes]
rs9991203	0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107243400-107271400	Weak transcription	Right Ventricle	heart
2	chr4:107247000-107263600	Strong transcription	Fetal Thymus	thymus
3	chr4:107247000-107271400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:107247600-107263600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:107253200-107268200	Weak transcription	NHEK	skin
6	chr4:107255800-107266800	Weak transcription	Stomach Mucosa	stomach
7	chr4:107256200-107266200	Weak transcription	HMEC	breast
8	chr4:107258600-107281400	Weak transcription	Fetal Heart	heart
9	chr4:107259000-107267600	Weak transcription	K562	blood
10	chr4:107259200-107265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:107259600-107270600	Weak transcription	Brain Substantia Nigra	brain
12	chr4:107259800-107266600	Strong transcription	Primary B cells from cord blood	blood
13	chr4:107259800-107272400	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:107260000-107272200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:107260200-107265600	Weak transcription	Small Intestine	intestine
16	chr4:107260200-107265800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:107260200-107267600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:107260200-107268000	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:107260200-107268000	Weak transcription	Gastric	stomach
20	chr4:107260200-107269800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr4:107260200-107269800	Weak transcription	Fetal Brain Male	brain
22	chr4:107260200-107269800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:107260200-107270400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:107260200-107270600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:107260200-107271800	Weak transcription	Lung	lung
26	chr4:107260200-107272600	Weak transcription	Fetal Intestine Small	intestine
27	chr4:107260200-107274400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:107260200-107274400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:107260200-107275800	Weak transcription	Spleen	Spleen
30	chr4:107260200-107276000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:107260200-107276600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:107260200-107276800	Weak transcription	Psoas Muscle	Psoas
33	chr4:107260400-107265200	Weak transcription	NHLF	lung
34	chr4:107260400-107268000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:107260400-107268800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:107260400-107268800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr4:107260400-107269400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:107260400-107274400	Weak transcription	Brain Germinal Matrix	brain
39	chr4:107260400-107276000	Weak transcription	Brain Angular Gyrus	brain
40	chr4:107260400-107276600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr4:107260600-107265600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:107260600-107267600	Weak transcription	Adipose Nuclei	Adipose
43	chr4:107260600-107268600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr4:107260600-107269800	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:107260800-107265200	Weak transcription	Osteobl	bone
46	chr4:107260800-107266200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:107260800-107267600	Weak transcription	Placenta	Placenta
48	chr4:107260800-107267800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr4:107260800-107268000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:107260800-107268200	Weak transcription	HUVEC	blood vessel

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