Variant report

Variant	rs34489202
Chromosome Location	chr3:98599565-98599566
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	chr3:98597641..98599720-chr3:98602345..98604464,2	K562	blood:
2	chr3:98595066..98597311-chr3:98599043..98600864,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10428160	0.91[EUR][1000 genomes]
rs10589669	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11552978	0.87[EUR][1000 genomes]
rs12107272	0.95[EUR][1000 genomes]
rs12108018	0.98[EUR][1000 genomes]
rs12108142	0.89[EUR][1000 genomes]
rs13059624	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13065136	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13068317	0.93[EUR][1000 genomes]
rs13072410	0.89[EUR][1000 genomes]
rs13074614	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13074787	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13076960	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13078549	0.91[EUR][1000 genomes]
rs13079960	0.82[EUR][1000 genomes]
rs13080057	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13081992	0.95[EUR][1000 genomes]
rs13083238	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083613	0.87[EUR][1000 genomes]
rs13083934	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13084692	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13087627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13087631	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13088532	0.86[EUR][1000 genomes]
rs13091170	0.95[EUR][1000 genomes]
rs13091236	0.89[EUR][1000 genomes]
rs13093128	0.87[EUR][1000 genomes]
rs13096085	0.95[EUR][1000 genomes]
rs13097876	0.95[EUR][1000 genomes]
rs13100915	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13100937	0.95[EUR][1000 genomes]
rs1983009	0.82[EUR][1000 genomes]
rs2439232	0.89[EUR][1000 genomes]
rs2454687	0.87[EUR][1000 genomes]
rs34008360	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34269725	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34279227	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34284740	0.95[EUR][1000 genomes]
rs34394867	0.91[EUR][1000 genomes]
rs34428696	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34458031	0.83[AMR][1000 genomes]
rs34470469	0.85[EUR][1000 genomes]
rs34479374	0.82[EUR][1000 genomes]
rs34688367	0.98[EUR][1000 genomes]
rs34711372	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34725039	0.95[EUR][1000 genomes]
rs34791359	0.83[AMR][1000 genomes]
rs34826460	0.95[EUR][1000 genomes]
rs34848749	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34860591	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35006699	0.98[EUR][1000 genomes]
rs35025156	0.95[EUR][1000 genomes]
rs35076733	0.95[EUR][1000 genomes]
rs35098355	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35103318	0.95[EUR][1000 genomes]
rs35219252	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35234681	0.93[EUR][1000 genomes]
rs35239055	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35312318	0.95[EUR][1000 genomes]
rs35366262	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35422064	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35499232	0.95[EUR][1000 genomes]
rs35514544	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35526367	0.91[EUR][1000 genomes]
rs35539438	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35592768	0.91[EUR][1000 genomes]
rs35764973	0.95[EUR][1000 genomes]
rs35854439	0.84[EUR][1000 genomes]
rs35894621	0.83[AMR][1000 genomes]
rs35914268	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35947493	0.82[EUR][1000 genomes]
rs35947806	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36028944	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs36032715	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36098932	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36157152	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36160001	0.86[EUR][1000 genomes]
rs36175276	0.86[EUR][1000 genomes]
rs41267851	0.86[EUR][1000 genomes]
rs55644421	0.98[EUR][1000 genomes]
rs56083233	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56094988	0.84[EUR][1000 genomes]
rs56246599	0.95[EUR][1000 genomes]
rs56408882	0.91[EUR][1000 genomes]
rs6764579	0.93[EUR][1000 genomes]
rs6805362	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71124004	0.81[EUR][1000 genomes]
rs71311393	0.89[EUR][1000 genomes]
rs71311394	0.89[EUR][1000 genomes]
rs71311397	0.87[EUR][1000 genomes]
rs71311398	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71311402	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313504	0.95[EUR][1000 genomes]
rs71313506	0.89[EUR][1000 genomes]
rs71313508	0.95[EUR][1000 genomes]
rs71313509	0.95[EUR][1000 genomes]
rs71313510	0.95[EUR][1000 genomes]
rs71313511	0.95[EUR][1000 genomes]
rs71313512	0.83[AMR][1000 genomes]
rs7614053	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv3441569	chr3:98585311-98607020	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98567600-98601000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr3:98575400-98603800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:98575800-98603200	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:98575800-98603800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98578000-98601000	Weak transcription	Lung	lung
6	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:98584400-98607200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:98584600-98604200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:98587200-98604600	Weak transcription	Ovary	ovary
10	chr3:98587800-98601800	Strong transcription	HSMM	muscle
11	chr3:98589200-98602200	Weak transcription	NHLF	lung
12	chr3:98589400-98609200	Weak transcription	Fetal Intestine Large	intestine
13	chr3:98589600-98599800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:98589800-98604000	Weak transcription	Fetal Stomach	stomach
15	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
16	chr3:98590800-98604600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:98591400-98602200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:98591400-98604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:98591600-98600000	Weak transcription	Dnd41	blood
20	chr3:98591600-98604600	Weak transcription	Aorta	Aorta
21	chr3:98592600-98604600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:98593800-98604600	Weak transcription	Psoas Muscle	Psoas
23	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
24	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
25	chr3:98594600-98600600	Strong transcription	HUVEC	blood vessel
26	chr3:98594600-98602200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr3:98594600-98604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:98595000-98603600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:98595200-98608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:98595600-98600400	Genic enhancers	NHEK	skin
31	chr3:98595600-98601800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:98596000-98604000	Weak transcription	K562	blood
33	chr3:98596200-98600800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:98596200-98601000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:98596200-98606600	Weak transcription	HepG2	liver
36	chr3:98596600-98600600	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr3:98596800-98604200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:98597000-98600400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:98597000-98600400	Strong transcription	Fetal Lung	lung
40	chr3:98597000-98609000	Weak transcription	Right Ventricle	heart
41	chr3:98597200-98600000	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:98597400-98599800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:98597600-98602400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:98597600-98602800	Strong transcription	HMEC	breast
46	chr3:98597800-98602800	Strong transcription	Osteobl	bone
47	chr3:98597800-98604200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:98598000-98600600	Weak transcription	Placenta	Placenta
49	chr3:98598000-98603800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:98598200-98602200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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