Variant report

Variant	rs12641113
Chromosome Location	chr4:106086302-106086303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106077302..106081599-chr4:106085488..106089334,5	MCF-7	breast:
2	chr4:106086235..106088556-chr4:106151811..106153985,2	MCF-7	breast:
3	chr4:106079358..106082309-chr4:106085519..106087044,2	MCF-7	breast:
4	chr4:106066054..106072074-chr4:106082791..106088077,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10010281	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10014102	0.96[ASN][1000 genomes]
rs10022109	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12643257	0.92[ASN][1000 genomes]
rs12645165	0.93[ASN][1000 genomes]
rs12647922	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17617028	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2189234	0.91[ASN][1000 genomes]
rs2285720	1.00[ASN][1000 genomes]
rs35515350	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62331150	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62331151	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs974801	0.91[ASN][1000 genomes]
rs9790517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884482	0.97[ASN][1000 genomes]
rs988799	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106087600	Weak transcription	Lung	lung
2	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
3	chr4:106069600-106102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:106069800-106101000	Weak transcription	HSMM	muscle
5	chr4:106069800-106101800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:106070400-106111600	Weak transcription	Placenta	Placenta
8	chr4:106071000-106100800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:106072600-106100600	Weak transcription	Adipose Nuclei	Adipose
10	chr4:106076200-106089200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:106076200-106092800	Weak transcription	Psoas Muscle	Psoas
12	chr4:106076200-106093000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:106077000-106100800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
15	chr4:106078000-106092200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
17	chr4:106080200-106091400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:106080400-106088800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr4:106080400-106088800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr4:106080600-106086400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:106080600-106101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:106080600-106102800	Weak transcription	NHEK	skin
23	chr4:106080600-106105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:106080600-106107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:106080800-106091000	Weak transcription	Ovary	ovary
26	chr4:106080800-106095200	Weak transcription	Fetal Intestine Large	intestine
27	chr4:106081000-106087000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:106081000-106089400	Weak transcription	Fetal Intestine Small	intestine
29	chr4:106083400-106091400	Weak transcription	Primary T cells from cord blood	blood
30	chr4:106083600-106089200	Weak transcription	Small Intestine	intestine
31	chr4:106083600-106097200	ZNF genes & repeats	GM12878-XiMat	blood
32	chr4:106083600-106100800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:106083600-106100800	Weak transcription	Right Ventricle	heart
34	chr4:106083600-106109200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:106083800-106089000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:106083800-106089200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:106083800-106089400	Weak transcription	Fetal Brain Male	brain
38	chr4:106083800-106091400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:106083800-106092800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr4:106083800-106092800	Weak transcription	Brain Anterior Caudate	brain
41	chr4:106083800-106095600	Weak transcription	Fetal Muscle Leg	muscle
42	chr4:106083800-106095800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:106083800-106100400	Weak transcription	Stomach Mucosa	stomach
44	chr4:106083800-106104800	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr4:106083800-106111400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:106084000-106105000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:106084600-106086800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:106084600-106092800	Weak transcription	K562	blood
49	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
50	chr4:106085200-106086600	Strong transcription	Primary B cells from cord blood	blood

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