Variant report

Variant	rs1800024
Chromosome Location	chr3:46412559-46412560
allele	C/T
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	BATF	chr3:46412238-46412651	GM12878	blood:	n/a	n/a
2	NFIC	chr3:46412153-46412810	GM12878	blood:	n/a	n/a
3	GATA3	chr3:46412338-46412917	T-47D	breast:	n/a	chr3:46412610-46412617 chr3:46412610-46412620
4	UBTF	chr3:46412474-46412572	K562	blood:	n/a	n/a

Variant related genes	Relation type
CCR5	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10510751	0.87[EUR][1000 genomes]
rs12495098	0.81[EUR][1000 genomes]
rs17141006	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17141010	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1799864	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1894389	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34138562	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35728689	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3918357	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3918363	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3918364	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62242983	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62242995	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62246129	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62246130	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46396000-46422000	Weak transcription	Lung	lung
2	chr3:46404400-46422200	Weak transcription	Thymus	Thymus
3	chr3:46404400-46424600	Weak transcription	Spleen	Spleen
4	chr3:46409200-46413200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr3:46409400-46414200	Enhancers	Fetal Thymus	thymus
6	chr3:46409400-46418600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:46409600-46412800	Enhancers	Primary T cells from cord blood	blood
8	chr3:46409600-46417200	Enhancers	Dnd41	blood
9	chr3:46409800-46412600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:46410000-46412600	Active TSS	Brain Hippocampus Middle	brain
11	chr3:46410000-46413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:46410000-46414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:46410200-46420000	Weak transcription	Primary B cells from cord blood	blood
14	chr3:46411000-46412600	Enhancers	Fetal Lung	lung
15	chr3:46411000-46412800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr3:46411200-46413200	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:46411200-46413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:46411400-46412600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:46411400-46413000	Weak transcription	Placenta	Placenta
20	chr3:46411400-46416800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr3:46411400-46422000	Weak transcription	Small Intestine	intestine
22	chr3:46411600-46413000	Enhancers	GM12878-XiMat	blood
23	chr3:46411600-46413600	Active TSS	Fetal Muscle Leg	muscle
24	chr3:46411800-46412600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr3:46411800-46413200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:46412000-46412600	Enhancers	Fetal Stomach	stomach
27	chr3:46412000-46412800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:46412000-46413000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:46412000-46413400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:46412000-46416600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:46412200-46412600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:46412200-46413200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:46412200-46413400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr3:46412200-46413400	Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:46412200-46414200	Active TSS	Duodenum Mucosa	Duodenum
36	chr3:46412200-46415400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:46412400-46412600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:46412400-46412600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:46412400-46412600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:46412400-46412600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:46412400-46413000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:46412400-46413600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:46412400-46415000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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