Variant report

Variant	rs10489125
Chromosome Location	chr4:99507836-99507837
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	chr4:99499694..99502354-chr4:99504624..99508480,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10026446	0.82[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10516433	0.82[JPT][hapmap]
rs10516434	0.82[JPT][hapmap]
rs1528548	0.84[AMR][1000 genomes]
rs1547382	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1554849	0.82[JPT][hapmap]
rs17027799	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17027802	0.90[CHB][hapmap]
rs17027806	1.00[ASW][hapmap];0.83[LWK][hapmap];0.81[AMR][1000 genomes]
rs17498778	1.00[JPT][hapmap]
rs17499015	0.82[JPT][hapmap]
rs17564872	0.82[JPT][hapmap]
rs4699654	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs62323626	0.83[ASN][1000 genomes]
rs62323627	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62323629	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62323632	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62323633	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532740	0.82[JPT][hapmap]
rs6532746	0.82[JPT][hapmap]
rs6833529	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6840610	0.82[JPT][hapmap]
rs6853079	0.82[JPT][hapmap]
rs7666585	1.00[JPT][hapmap]
rs7667273	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs7689289	0.82[JPT][hapmap]
rs950152	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99490800-99509000	Weak transcription	HSMM	muscle
2	chr4:99497200-99510200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:99498600-99508000	Enhancers	Brain Anterior Caudate	brain
4	chr4:99500000-99508000	Weak transcription	Spleen	Spleen
5	chr4:99500400-99508000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:99500800-99508000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:99502200-99508200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr4:99502600-99508000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:99502600-99508000	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:99503400-99508000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:99503600-99508000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:99503600-99508000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:99503600-99508000	Weak transcription	Gastric	stomach
14	chr4:99504200-99509200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:99505000-99510400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:99505200-99508000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:99505200-99510200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:99505400-99508000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:99505600-99508000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:99506400-99509600	Enhancers	Fetal Brain Male	brain
21	chr4:99506800-99508000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:99506800-99508000	Enhancers	Brain Germinal Matrix	brain
23	chr4:99506800-99508400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:99506800-99509600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:99507000-99508000	Weak transcription	Esophagus	oesophagus
26	chr4:99507000-99508200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr4:99507000-99508200	Enhancers	HMEC	breast
28	chr4:99507000-99508200	Enhancers	NHEK	skin
29	chr4:99507000-99508400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:99507000-99508400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:99507000-99508400	Enhancers	Fetal Lung	lung
32	chr4:99507000-99508600	Enhancers	Fetal Heart	heart
33	chr4:99507000-99509000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:99507000-99513600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:99507200-99508200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr4:99507200-99508400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:99507200-99508600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:99507200-99508600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:99507200-99509400	Weak transcription	NHDF-Ad	bronchial
40	chr4:99507400-99510200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:99507600-99508000	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr4:99507600-99508600	Enhancers	Ovary	ovary
43	chr4:99507600-99509000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:99507600-99510400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:99507800-99508200	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr4:99507800-99508200	Enhancers	Lung	lung
47	chr4:99507800-99508400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr4:99507800-99508400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:99507800-99508400	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr4:99507800-99508400	Flanking Active TSS	Brain Substantia Nigra	brain

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