Variant report

Variant	rs3898322
Chromosome Location	chr4:90709490-90709491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10516846	0.97[AFR][1000 genomes]
rs10516847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233696	1.00[CEU][hapmap]
rs12502730	1.00[CEU][hapmap]
rs1442132	1.00[CEU][hapmap]
rs17016074	1.00[YRI][hapmap]
rs17016083	0.84[AFR][1000 genomes]
rs17016100	1.00[YRI][hapmap]
rs17016124	0.96[AFR][1000 genomes]
rs17016126	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17016188	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17016193	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17016196	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016235	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2298727	0.98[ASN][1000 genomes]
rs2298728	0.98[ASN][1000 genomes]
rs2870027	0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34164595	1.00[ASN][1000 genomes]
rs34238791	0.97[ASN][1000 genomes]
rs34351491	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs34356244	0.96[AFR][1000 genomes]
rs35540244	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35683448	0.84[AFR][1000 genomes]
rs35897584	0.98[ASN][1000 genomes]
rs35921673	0.90[AFR][1000 genomes]
rs3729594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775453	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796662	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796667	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3822088	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3857060	1.00[YRI][hapmap]
rs58877857	0.96[AFR][1000 genomes]
rs6532190	0.81[CHB][hapmap];0.91[JPT][hapmap];1.00[ASN][1000 genomes]
rs6532200	1.00[CEU][hapmap]
rs6825073	0.97[AFR][1000 genomes]
rs6842093	1.00[YRI][hapmap]
rs72657741	0.94[AFR][1000 genomes]
rs7699596	0.97[AFR][1000 genomes]
rs894278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs961386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90687200-90718400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:90697000-90711000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:90703000-90712600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:90705600-90718400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:90706400-90733800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:90707800-90721400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:90709000-90710200	Enhancers	Fetal Heart	heart
8	chr4:90709200-90709600	Enhancers	Brain Substantia Nigra	brain
9	chr4:90709200-90709800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:90709200-90709800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:90709200-90709800	Enhancers	Brain Anterior Caudate	brain
12	chr4:90709200-90709800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr4:90709200-90709800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:90709200-90709800	Flanking Active TSS	Fetal Lung	lung
15	chr4:90709200-90709800	Enhancers	Ovary	ovary
16	chr4:90709200-90709800	Enhancers	Right Atrium	heart
17	chr4:90709200-90710200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:90709200-90711400	Enhancers	HUVEC	blood vessel
19	chr4:90709400-90709600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:90709400-90709800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:90709400-90709800	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr4:90709400-90709800	Enhancers	Left Ventricle	heart
23	chr4:90709400-90710000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:90709400-90710000	Enhancers	Right Ventricle	heart
25	chr4:90709400-90710000	Enhancers	HMEC	breast
26	chr4:90709400-90710200	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr4:90709400-90710200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:90709400-90710200	Enhancers	Brain Cingulate Gyrus	brain

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