Variant report

Variant	rs17012253
Chromosome Location	chr4:87919706-87919707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87918478..87926067-chr4:87926181..87931063,13	MCF-7	breast:
2	chr4:87852916..87856061-chr4:87919493..87922700,3	K562	blood:
3	chr4:87858278..87859821-chr4:87918030..87920940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1048482	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11930536	0.81[AFR][1000 genomes]
rs11937693	1.00[AMR][1000 genomes]
rs11939722	0.81[AFR][1000 genomes]
rs11943683	1.00[YRI][hapmap]
rs11944829	0.87[AFR][1000 genomes]
rs11945169	0.90[ASW][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap]
rs17012255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6810606	0.83[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6810840	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6827682	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6831823	0.90[ASW][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];0.93[YRI][hapmap]
rs6833094	0.93[YRI][hapmap]
rs6851927	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6857010	0.93[YRI][hapmap]
rs729984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7671609	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs7677039	0.92[YRI][hapmap]
rs7677287	0.93[YRI][hapmap];0.90[AFR][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	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers 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 target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription 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	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87882600-87920200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:87895400-87920000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:87899200-87922800	Weak transcription	Osteobl	bone
10	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
11	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:87900000-87924400	Weak transcription	NHEK	skin
13	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:87903600-87919800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:87903600-87921000	Weak transcription	Primary T cells from cord blood	blood
17	chr4:87903800-87919800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:87903800-87920000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:87904400-87920000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr4:87904600-87921000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:87905800-87920200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:87907600-87920000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:87910000-87921200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:87912800-87920600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:87914200-87927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:87915800-87919800	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:87915800-87919800	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:87915800-87920000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:87915800-87920000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr4:87915800-87920600	Weak transcription	Brain Anterior Caudate	brain
32	chr4:87915800-87921000	Weak transcription	Small Intestine	intestine
33	chr4:87916000-87920000	Weak transcription	Psoas Muscle	Psoas
34	chr4:87916000-87920200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr4:87916000-87920600	Weak transcription	Ovary	ovary
36	chr4:87916000-87921000	Weak transcription	Stomach Mucosa	stomach
37	chr4:87916000-87926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:87916200-87920000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr4:87916200-87920000	Weak transcription	Right Atrium	heart
40	chr4:87916200-87920000	Weak transcription	Thymus	Thymus
41	chr4:87916200-87920000	Weak transcription	Spleen	Spleen
42	chr4:87916200-87920000	Weak transcription	Dnd41	blood
43	chr4:87916200-87920800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:87916200-87921000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:87916200-87922800	Weak transcription	Lung	lung
46	chr4:87916200-87927200	Weak transcription	Esophagus	oesophagus
47	chr4:87916400-87920000	Weak transcription	Liver	Liver
48	chr4:87916400-87920000	Weak transcription	Fetal Thymus	thymus
49	chr4:87916400-87920000	Weak transcription	HepG2	liver
50	chr4:87916400-87920000	Weak transcription	K562	blood

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