Variant report

Variant	rs13110999
Chromosome Location	chr4:110363644-110363645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110353268..110357375-chr4:110361363..110366275,8	MCF-7	breast:
2	chr4:110358554..110360158-chr4:110363146..110366094,2	MCF-7	breast:
3	chr4:110362207..110365023-chr4:110395130..110397808,3	K562	blood:
4	chr4:110353905..110356378-chr4:110363293..110365654,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138802	Chromatin interaction
ENSG00000247950	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10000545	0.86[CEU][hapmap]
rs10002595	0.86[CEU][hapmap]
rs10016533	0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.97[EUR][1000 genomes]
rs10025781	0.93[EUR][1000 genomes]
rs10155127	0.86[CEU][hapmap]
rs10213562	0.95[GIH][hapmap]
rs10452150	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10516558	0.93[CEU][hapmap]
rs11929713	0.81[CEU][hapmap];1.00[MEX][hapmap]
rs11930655	0.85[CEU][hapmap]
rs11942291	0.86[CEU][hapmap]
rs11942858	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs12643055	0.86[CEU][hapmap]
rs12648965	0.86[CEU][hapmap]
rs13103034	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs13122093	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13123618	0.86[CEU][hapmap]
rs13128221	0.93[CEU][hapmap]
rs13128445	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs13132816	0.93[EUR][1000 genomes]
rs13133491	0.93[EUR][1000 genomes]
rs13140373	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs13142698	0.85[CEU][hapmap]
rs13143825	0.93[CEU][hapmap]
rs13145066	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs13151464	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13151516	0.93[EUR][1000 genomes]
rs1509314	0.86[CEU][hapmap]
rs1509315	0.93[CEU][hapmap]
rs15821	0.93[EUR][1000 genomes]
rs17040436	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs17040439	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs17040461	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs17040510	0.80[CEU][hapmap]
rs28681408	0.86[CEU][hapmap]
rs33911248	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34132975	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34133579	0.93[EUR][1000 genomes]
rs34320670	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34368920	0.82[EUR][1000 genomes]
rs34473874	0.85[EUR][1000 genomes]
rs34502105	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34660885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34710885	0.93[EUR][1000 genomes]
rs34727629	0.93[EUR][1000 genomes]
rs34813537	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34851707	0.93[EUR][1000 genomes]
rs34861128	0.90[EUR][1000 genomes]
rs34953524	0.93[EUR][1000 genomes]
rs35199349	0.93[EUR][1000 genomes]
rs35273490	0.81[EUR][1000 genomes]
rs35313553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35329136	0.93[EUR][1000 genomes]
rs35450490	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35598950	0.93[EUR][1000 genomes]
rs35699695	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35829490	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35865655	0.84[EUR][1000 genomes]
rs35866656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35950484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36102563	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41277037	0.93[EUR][1000 genomes]
rs6533427	0.81[EUR][1000 genomes]
rs6533434	0.85[CEU][hapmap];1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs66493839	0.93[EUR][1000 genomes]
rs67066117	0.89[EUR][1000 genomes]
rs67727505	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67923759	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6825928	0.86[MEX][hapmap]
rs6828719	0.84[EUR][1000 genomes]
rs6834685	0.82[EUR][1000 genomes]
rs6835683	0.86[CEU][hapmap]
rs6841198	0.86[CEU][hapmap]
rs6856291	0.93[CEU][hapmap]
rs714586	0.85[CEU][hapmap]
rs71603034	0.92[EUR][1000 genomes]
rs71603035	0.84[EUR][1000 genomes]
rs72672698	0.84[EUR][1000 genomes]
rs7436583	0.86[CEU][hapmap]
rs7440570	0.86[CEU][hapmap]
rs7675602	0.86[CEU][hapmap]
rs7694710	0.92[EUR][1000 genomes]
rs9985632	0.86[CEU][hapmap]
rs9994676	0.80[CEU][hapmap]
rs9999570	0.86[CEU][hapmap]

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:121 , 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	chr4:110356600-110364400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr4:110356800-110366000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:110357200-110366000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:110357400-110364400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:110357400-110365200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr4:110357400-110365800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:110357400-110366200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:110357400-110367200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:110357600-110364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:110357600-110367200	Weak transcription	Fetal Kidney	kidney
12	chr4:110357800-110366200	Weak transcription	Fetal Stomach	stomach
13	chr4:110357800-110366400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr4:110357800-110370600	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr4:110358000-110364800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:110358000-110366000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:110358000-110366000	Weak transcription	Fetal Intestine Small	intestine
18	chr4:110358000-110366200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:110358000-110366800	Weak transcription	Fetal Intestine Large	intestine
20	chr4:110358000-110367200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:110358000-110370600	Weak transcription	Fetal Brain Female	brain
22	chr4:110358000-110372000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:110358000-110384000	Weak transcription	Fetal Brain Male	brain
24	chr4:110358000-110384200	Weak transcription	Colonic Mucosa	Colon
25	chr4:110358600-110378600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:110360200-110364800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr4:110360400-110364200	Weak transcription	Primary B cells from cord blood	blood
28	chr4:110360400-110364200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:110360400-110384200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr4:110360600-110364000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:110360600-110367200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:110361000-110364200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:110361200-110363800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr4:110361200-110364600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:110361200-110365400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr4:110361200-110366000	Enhancers	Primary T cells from cord blood	blood
37	chr4:110361400-110364600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:110361600-110363800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:110361600-110364600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr4:110361600-110364600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr4:110361600-110364800	Enhancers	Osteobl	bone
42	chr4:110361600-110365000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr4:110361600-110365200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:110361600-110365200	Enhancers	Colon Smooth Muscle	Colon
45	chr4:110361600-110365600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr4:110361800-110363800	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:110361800-110363800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:110361800-110363800	Enhancers	HSMM	muscle
49	chr4:110361800-110365000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr4:110361800-110366000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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