Variant report

Variant	rs2254089
Chromosome Location	chr3:46413418-46413419
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	RCOR1	chr3:46413366-46413621	K562	blood:	n/a	n/a
2	ZNF143	chr3:46413368-46413656	K562	blood:	n/a	n/a

Variant related genes	Relation type
CCR5	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11266744	0.82[EUR][1000 genomes]
rs11574433	0.82[AFR][1000 genomes]
rs11575815	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11575816	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1799987	0.82[ASN][1000 genomes]
rs1799988	0.86[ASN][1000 genomes]
rs1800023	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800874	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187674	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2213290	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2734225	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2734648	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856757	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2856764	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087252	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3181039	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3204849	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34682274	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41515644	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4560336	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4683220	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683223	0.81[EUR][1000 genomes]
rs66484806	0.81[EUR][1000 genomes]
rs746492	0.82[ASN][1000 genomes]
rs916091	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[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:38 , 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	chr3:46409400-46414200	Enhancers	Fetal Thymus	thymus
5	chr3:46409400-46418600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr3:46409600-46417200	Enhancers	Dnd41	blood
7	chr3:46410000-46414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:46410200-46420000	Weak transcription	Primary B cells from cord blood	blood
9	chr3:46411400-46416800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:46411400-46422000	Weak transcription	Small Intestine	intestine
11	chr3:46411600-46413600	Active TSS	Fetal Muscle Leg	muscle
12	chr3:46412000-46416600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:46412200-46414200	Active TSS	Duodenum Mucosa	Duodenum
14	chr3:46412200-46415400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:46412400-46413600	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr3:46412400-46415000	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr3:46412600-46413600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:46412600-46413600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:46412600-46415400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:46412600-46416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr3:46412800-46415800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:46412800-46416200	Weak transcription	Primary T cells from cord blood	blood
23	chr3:46413000-46414000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:46413000-46415400	Enhancers	Placenta	Placenta
25	chr3:46413200-46413600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr3:46413200-46414200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr3:46413200-46414600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:46413200-46414800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:46413200-46415000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:46413200-46415800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr3:46413400-46413600	Active TSS	Primary monocytes fromperipheralblood	blood
32	chr3:46413400-46413600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:46413400-46413600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr3:46413400-46413600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:46413400-46413600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:46413400-46413800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr3:46413400-46413800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
38	chr3:46413400-46413800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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