Variant report

Variant	rs1799987
Chromosome Location	chr3:46411935-46411936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr3:46410898-46411959	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CCR5	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1001007	0.85[ASN][1000 genomes]
rs1799988	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1800023	0.80[ASN][1000 genomes]
rs1800874	0.81[ASN][1000 genomes]
rs2187673	0.85[ASN][1000 genomes]
rs2254089	0.82[ASN][1000 genomes]
rs2734648	0.82[ASN][1000 genomes]
rs2856764	0.82[ASN][1000 genomes]
rs2856765	0.82[ASN][1000 genomes]
rs35060576	0.85[ASN][1000 genomes]
rs6441974	0.85[ASN][1000 genomes]
rs746492	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46396000-46422000	Weak transcription	Lung	lung
2	chr3:46404400-46412400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:46404400-46422200	Weak transcription	Thymus	Thymus
4	chr3:46404400-46424600	Weak transcription	Spleen	Spleen
5	chr3:46407000-46412200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:46408400-46412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:46409000-46412200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr3:46409200-46412000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:46409200-46413200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:46409400-46412000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:46409400-46412200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:46409400-46414200	Enhancers	Fetal Thymus	thymus
13	chr3:46409400-46418600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:46409600-46412800	Enhancers	Primary T cells from cord blood	blood
15	chr3:46409600-46417200	Enhancers	Dnd41	blood
16	chr3:46409800-46412600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:46410000-46412600	Active TSS	Brain Hippocampus Middle	brain
18	chr3:46410000-46413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:46410000-46414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:46410200-46412400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:46410200-46420000	Weak transcription	Primary B cells from cord blood	blood
22	chr3:46411000-46412200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:46411000-46412600	Enhancers	Fetal Lung	lung
24	chr3:46411000-46412800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:46411200-46412000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr3:46411200-46413200	Enhancers	Primary hematopoietic stem cells	blood
27	chr3:46411200-46413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:46411400-46412200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:46411400-46412600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:46411400-46413000	Weak transcription	Placenta	Placenta
31	chr3:46411400-46416800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:46411400-46422000	Weak transcription	Small Intestine	intestine
33	chr3:46411600-46412200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:46411600-46413000	Enhancers	GM12878-XiMat	blood
35	chr3:46411600-46413600	Active TSS	Fetal Muscle Leg	muscle
36	chr3:46411800-46412600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr3:46411800-46413200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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