Variant report

Variant	rs4488940
Chromosome Location	chr4:102231056-102231057
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:101039108..101041675-chr4:102229054..102231223,2	K562	blood:
2	chr4:102229146..102231940-chr4:102232073..102233783,2	K562	blood:

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	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs1441431	0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1441434	1.00[AMR][1000 genomes]
rs1561722	0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17031168	0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031172	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031175	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031176	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031180	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs17031182	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3974659	0.90[AFR][1000 genomes];0.91[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	0.86[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	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs6812094	0.93[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]
rs6828025	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	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6831824	0.81[AFR][1000 genomes]
rs6832020	0.93[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	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6842191	0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6844844	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6846554	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6852282	0.90[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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102215000-102232600	Weak transcription	Pancreas	Pancrea
2	chr4:102215400-102236600	Weak transcription	Primary B cells from cord blood	blood
3	chr4:102222000-102232800	Weak transcription	Lung	lung
4	chr4:102226400-102232600	Weak transcription	Left Ventricle	heart
5	chr4:102227800-102238200	Weak transcription	Right Ventricle	heart
6	chr4:102228200-102231200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:102228200-102249400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:102228200-102250400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:102228600-102231200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:102228600-102232600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:102228600-102232600	Weak transcription	Ovary	ovary
12	chr4:102228600-102232600	Weak transcription	Spleen	Spleen
13	chr4:102228600-102234000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:102228600-102241800	Weak transcription	HSMM	muscle
15	chr4:102228600-102247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:102228800-102232200	Weak transcription	A549	lung
17	chr4:102228800-102232400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:102228800-102235200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr4:102229000-102231200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:102229000-102234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:102229200-102234400	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:102229400-102234400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:102229600-102232200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:102229800-102232600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:102229800-102236600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:102230000-102231400	Enhancers	Brain Anterior Caudate	brain
27	chr4:102230000-102231800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr4:102230200-102232600	Weak transcription	Gastric	stomach
29	chr4:102230200-102234400	Weak transcription	Psoas Muscle	Psoas
30	chr4:102230400-102234400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:102230400-102236800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:102230600-102242600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:102230800-102231600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:102230800-102231800	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr4:102230800-102236800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr4:102230800-102241600	Weak transcription	Small Intestine	intestine
37	chr4:102231000-102231400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr4:102231000-102231400	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr4:102231000-102231800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr4:102231000-102238800	Weak transcription	Stomach Mucosa	stomach

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