Variant report

Variant	rs2856757
Chromosome Location	chr3:46410494-46410495
allele	A/C
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	RAD21	chr3:46410081-46410504	GM12878	blood:	n/a	n/a
2	CTCF	chr3:46410162-46410499	K562	blood:	n/a	chr3:46410284-46410302
3	CTCF	chr3:46410034-46410496	MCF-7	breast:	n/a	chr3:46410284-46410302
4	CTCF	chr3:46410440-46410590	HVMF	connective:	n/a	n/a
5	CTCF	chr3:46410300-46410590	HRPEpiC	eye:	n/a	n/a
6	RAD21	chr3:46409994-46410495	H1-hESC	embryonic stem cell:	n/a	n/a
7	RAD21	chr3:46410053-46410506	MCF-7	breast:	n/a	n/a
8	RAD21	chr3:46409958-46410502	HCT-116	colon:	n/a	n/a
9	CTCF	chr3:46410092-46410495	GM12878	blood:	n/a	chr3:46410284-46410302
10	CTCF	chr3:46410380-46410530	HCT-116	colon:	n/a	n/a
11	RAD21	chr3:46409922-46410503	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46129501..46130019-chr3:46409787..46410775,2	MCF-7	breast:
2	chr3:46334510..46335470-chr3:46409524..46410676,4	MCF-7	breast:
3	chr3:46249741..46250481-chr3:46410265..46410784,2	MCF-7	breast:
4	chr3:46249617..46250212-chr3:46410071..46410741,2	MCF-7	breast:

Variant related genes	Relation type
CCR5	TF binding region
ENSG00000163823	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11574433	0.82[AFR][1000 genomes]
rs11575815	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11575816	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1799988	0.83[ASN][1000 genomes]
rs1800023	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1800874	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187674	0.84[AFR][1000 genomes]
rs2213290	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2254089	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2734225	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2734648	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2856764	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2856765	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3087252	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3181039	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3204849	0.82[AFR][1000 genomes]
rs34682274	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41515644	0.96[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4560336	0.82[AFR][1000 genomes]
rs4683220	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs916091	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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:34 , 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	chr3:46404600-46411200	Weak transcription	Small Intestine	intestine
6	chr3:46407000-46411200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr3:46407000-46412200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:46408400-46412400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:46409000-46412200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:46409200-46412000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:46409200-46413200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:46409400-46410800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr3:46409400-46410800	Enhancers	GM12878-XiMat	blood
14	chr3:46409400-46411200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:46409400-46411400	Enhancers	Primary B cells from peripheral blood	blood
16	chr3:46409400-46412000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:46409400-46412200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:46409400-46414200	Enhancers	Fetal Thymus	thymus
19	chr3:46409400-46418600	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr3:46409600-46410600	Enhancers	Fetal Lung	lung
21	chr3:46409600-46412800	Enhancers	Primary T cells from cord blood	blood
22	chr3:46409600-46417200	Enhancers	Dnd41	blood
23	chr3:46409800-46410600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr3:46409800-46412600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:46410000-46411000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:46410000-46412600	Active TSS	Brain Hippocampus Middle	brain
27	chr3:46410000-46413200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:46410000-46414000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:46410200-46410600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:46410200-46411000	Weak transcription	Placenta	Placenta
31	chr3:46410200-46411600	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr3:46410200-46412400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:46410200-46420000	Weak transcription	Primary B cells from cord blood	blood
34	chr3:46410400-46411200	Weak transcription	Rectal Smooth Muscle	rectum

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