Variant report

Variant	rs17040433
Chromosome Location	chr4:110364903-110364904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110364092..110366042-chr4:110479951..110482299,2	K562	blood:
2	chr4:110363846..110365519-chr4:110386986..110389569,2	MCF-7	breast:
3	chr4:110353268..110357375-chr4:110361363..110366275,8	MCF-7	breast:
4	chr4:110358554..110360158-chr4:110363146..110366094,2	MCF-7	breast:
5	chr4:110362207..110365023-chr4:110395130..110397808,3	K562	blood:
6	chr4:110358792..110361560-chr4:110363855..110365822,2	K562	blood:
7	chr4:110353905..110356378-chr4:110363293..110365654,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138802	Chromatin interaction
ENSG00000247950	Chromatin interaction
ENSG00000005059	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10003981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10005225	1.00[EUR][1000 genomes]
rs10008457	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10009463	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10011971	1.00[EUR][1000 genomes]
rs10016533	0.89[LWK][hapmap]
rs10020652	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10030694	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040486	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs17040498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040565	1.00[CEU][hapmap]
rs28412073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28460762	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28541279	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595287	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28597954	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663368	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28680423	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723468	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829974	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57705376	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533431	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533432	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6812917	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6830772	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6834714	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837083	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6838597	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840561	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6852062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6854516	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898791	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7665738	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7667502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7674196	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7677736	1.00[CEU][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7681265	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685647	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7697001	1.00[CEU][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1836921	chr4:110354632-110370867	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv1839822	chr4:110354632-110370867	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110356400-110366200	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr4:110356800-110366000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:110357200-110366000	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr4:110357400-110365200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:110357400-110365800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:110357400-110366200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:110357400-110367200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:110357600-110367200	Weak transcription	Fetal Kidney	kidney
9	chr4:110357800-110366200	Weak transcription	Fetal Stomach	stomach
10	chr4:110357800-110366400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:110357800-110370600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr4:110358000-110366000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:110358000-110366000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:110358000-110366200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:110358000-110366800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:110358000-110367200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr4:110358000-110370600	Weak transcription	Fetal Brain Female	brain
18	chr4:110358000-110372000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr4:110358000-110384000	Weak transcription	Fetal Brain Male	brain
20	chr4:110358000-110384200	Weak transcription	Colonic Mucosa	Colon
21	chr4:110358600-110378600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr4:110360400-110384200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:110360600-110367200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:110361200-110365400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:110361200-110366000	Enhancers	Primary T cells from cord blood	blood
26	chr4:110361600-110365000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr4:110361600-110365200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:110361600-110365200	Enhancers	Colon Smooth Muscle	Colon
29	chr4:110361600-110365600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr4:110361800-110365000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr4:110361800-110366000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr4:110362000-110365600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr4:110362000-110367200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr4:110362200-110365000	Enhancers	Fetal Heart	heart
35	chr4:110362200-110366400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:110362200-110367200	Weak transcription	Brain Angular Gyrus	brain
37	chr4:110362800-110365000	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:110362800-110367200	Weak transcription	Right Ventricle	heart
39	chr4:110363000-110365000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:110363000-110365000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:110363000-110365000	Weak transcription	Lung	lung
42	chr4:110363000-110365400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr4:110363000-110366800	Weak transcription	Fetal Muscle Leg	muscle
44	chr4:110363000-110367000	Weak transcription	Brain Germinal Matrix	brain
45	chr4:110363000-110384200	Weak transcription	Esophagus	oesophagus
46	chr4:110363200-110365000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr4:110363200-110365200	Enhancers	GM12878-XiMat	blood
48	chr4:110363200-110367200	Weak transcription	Fetal Lung	lung
49	chr4:110363200-110367400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:110363200-110370600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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