Variant report

Variant	rs6828025
Chromosome Location	chr4:102242446-102242447
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1011849	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11943655	1.00[AMR][1000 genomes]
rs11946103	1.00[AMR][1000 genomes]
rs1372243	0.92[AFR][1000 genomes]
rs1372244	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs1441431	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1441434	1.00[AMR][1000 genomes]
rs1561722	0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17031168	0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031172	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031175	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031176	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031180	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031182	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3974659	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4488940	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4504259	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4637408	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55667372	0.88[AFR][1000 genomes]
rs58629361	0.88[AFR][1000 genomes]
rs59079781	0.92[AFR][1000 genomes]
rs59224049	0.88[AFR][1000 genomes]
rs59763039	0.88[AFR][1000 genomes]
rs60438397	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs60984918	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6532924	0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6532925	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6532926	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6810812	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs6812094	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6817805	0.81[AFR][1000 genomes]
rs6827528	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6830390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6831471	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6831824	0.81[AFR][1000 genomes]
rs6832020	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6834721	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6837858	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6842191	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6844844	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6846554	0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6852282	0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835916	1.00[AMR][1000 genomes]
rs73835923	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835924	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835932	0.91[AMR][1000 genomes]
rs73835933	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835934	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73835935	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835936	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835937	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835938	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73835939	0.88[AFR][1000 genomes]
rs73835940	0.88[AFR][1000 genomes]
rs73835941	0.88[AFR][1000 genomes]
rs73835943	0.87[AFR][1000 genomes]
rs73835944	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7655806	1.00[AMR][1000 genomes]
rs7661895	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7664396	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7671524	0.82[AFR][1000 genomes];0.82[AMR][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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv879676	chr4:102202285-102340930	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102228200-102249400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:102228200-102250400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:102228600-102247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:102230600-102242600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:102237400-102242600	Weak transcription	Primary B cells from cord blood	blood
6	chr4:102237400-102243600	Weak transcription	Psoas Muscle	Psoas
7	chr4:102237400-102247200	Weak transcription	Primary T cells from cord blood	blood
8	chr4:102237600-102243400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:102238400-102244400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:102241400-102243600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:102241600-102242600	Enhancers	Adipose Nuclei	Adipose
12	chr4:102241600-102243200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:102241600-102243600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:102241600-102243800	Enhancers	Ovary	ovary
15	chr4:102241800-102242600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:102241800-102242600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr4:102241800-102242800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:102241800-102243200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:102241800-102243200	Enhancers	NHEK	skin
20	chr4:102241800-102243400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:102241800-102243600	Enhancers	HMEC	breast
22	chr4:102241800-102243800	Enhancers	Colon Smooth Muscle	Colon
23	chr4:102242000-102242600	Weak transcription	Brain Hippocampus Middle	brain
24	chr4:102242000-102242800	Weak transcription	Brain Angular Gyrus	brain
25	chr4:102242000-102243200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr4:102242000-102243600	Enhancers	Brain Anterior Caudate	brain
27	chr4:102242000-102246800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:102242000-102247000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:102242200-102243200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr4:102242200-102243400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr4:102242200-102243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:102242400-102242600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr4:102242400-102242800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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