Variant report

Variant	rs10031904
Chromosome Location	chr4:99476005-99476006
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10000857	1.00[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10001528	0.97[EUR][1000 genomes]
rs10005706	1.00[CEU][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs10007752	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10010485	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10029528	1.00[CEU][hapmap]
rs10030396	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032578	1.00[CEU][hapmap]
rs17027682	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027758	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs17027760	1.00[CEU][hapmap]
rs17027826	1.00[CEU][hapmap]
rs17027841	1.00[CEU][hapmap]
rs17027845	1.00[CEU][hapmap]
rs1919212	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28372028	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28420592	0.83[EUR][1000 genomes]
rs28445981	0.97[EUR][1000 genomes]
rs28502504	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504661	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532945	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28550027	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28576181	1.00[EUR][1000 genomes]
rs28635613	0.93[EUR][1000 genomes]
rs28648419	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696298	0.83[EUR][1000 genomes]
rs28704122	0.83[EUR][1000 genomes]
rs28712025	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28758777	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902292	0.87[EUR][1000 genomes]
rs9990571	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9991086	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9993039	0.82[CHB][hapmap];0.97[EUR][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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99459200-99479600	Weak transcription	Spleen	Spleen
2	chr4:99463800-99478800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:99466400-99477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:99466600-99479800	Weak transcription	Fetal Thymus	thymus
5	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:99468400-99482200	Weak transcription	Esophagus	oesophagus
7	chr4:99468600-99477000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:99468600-99477000	Weak transcription	HMEC	breast
9	chr4:99468800-99476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:99468800-99476200	Weak transcription	Ovary	ovary
11	chr4:99468800-99476200	Weak transcription	NH-A	brain
12	chr4:99468800-99477000	Weak transcription	HSMMtube	muscle
13	chr4:99468800-99477200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:99469000-99476200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:99469000-99476600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:99469000-99482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:99474000-99477400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:99474000-99477400	Weak transcription	HSMM	muscle
19	chr4:99475200-99482400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:99475400-99478200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:99475400-99481400	Enhancers	Brain Hippocampus Middle	brain
22	chr4:99475400-99482000	Enhancers	Brain Cingulate Gyrus	brain
23	chr4:99475400-99482200	Enhancers	Brain Angular Gyrus	brain
24	chr4:99475600-99480600	Enhancers	Brain Germinal Matrix	brain
25	chr4:99475600-99481400	Enhancers	Brain Substantia Nigra	brain
26	chr4:99475800-99479200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:99475800-99479400	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr4:99475800-99482200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr4:99476000-99476200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr4:99476000-99477200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:99476000-99477400	Enhancers	Fetal Brain Male	brain
32	chr4:99476000-99477600	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr4:99476000-99477600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:99476000-99477800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr4:99476000-99477800	Enhancers	Brain Anterior Caudate	brain
36	chr4:99476000-99479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr4:99476000-99479200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr4:99476000-99479200	Enhancers	HUVEC	blood vessel
39	chr4:99476000-99479400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr4:99476000-99479600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr4:99476000-99479800	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr4:99476000-99481200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr4:99476000-99482200	Enhancers	Fetal Brain Female	brain

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