Variant report

Variant	rs28542885
Chromosome Location	chr2:9877661-9877662
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9855761..9857318-chr2:9876058..9878208,2	K562	blood:
2	chr15:79058374..79058894-chr2:9877496..9878033,2	MCF-7	breast:
3	chr2:9694952..9697993-chr2:9876014..9878927,3	MCF-7	breast:
4	chr1:245493743..245494253-chr2:9877159..9877996,2	MCF-7	breast:
5	chr2:9871478..9874528-chr2:9876144..9879356,3	K562	blood:

Variant related genes	Relation type
ENSG00000271855	Chromatin interaction
ENSG00000151694	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10164660	0.82[ASN][1000 genomes]
rs10929596	0.82[AMR][1000 genomes]
rs10929597	0.82[AMR][1000 genomes]
rs10929598	0.82[AMR][1000 genomes]
rs10929602	0.82[AMR][1000 genomes]
rs11892176	0.82[AMR][1000 genomes]
rs11901380	0.82[AMR][1000 genomes]
rs11902412	0.87[AMR][1000 genomes]
rs12472594	0.82[AMR][1000 genomes]
rs12991432	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1877949	0.83[ASN][1000 genomes]
rs1877950	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1877951	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357264	0.82[AMR][1000 genomes]
rs2357265	0.83[AMR][1000 genomes]
rs4459704	0.82[AMR][1000 genomes]
rs4668637	0.82[AMR][1000 genomes]
rs4668638	0.81[AMR][1000 genomes]
rs4668641	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4668642	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4668643	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669428	0.83[AMR][1000 genomes]
rs4669429	0.82[AMR][1000 genomes]
rs4669432	0.82[AMR][1000 genomes]
rs4669433	0.81[AMR][1000 genomes]
rs4669445	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4669446	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5020306	0.82[AMR][1000 genomes]
rs6432033	0.82[AMR][1000 genomes]
rs6712077	0.85[AMR][1000 genomes]
rs6727688	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6752842	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	esv3444702	chr2:9876876-9878974	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9875000-9879200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr2:9875000-9879200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr2:9875000-9879400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:9875000-9879400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr2:9875200-9877800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:9875200-9878800	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:9875200-9879000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr2:9875200-9879000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr2:9875200-9879000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr2:9875200-9879000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:9875200-9879400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:9875200-9879400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:9875400-9879000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:9875400-9879200	Enhancers	Primary T cells from cord blood	blood
15	chr2:9875800-9877800	Enhancers	Fetal Thymus	thymus
16	chr2:9875800-9879200	Weak transcription	Esophagus	oesophagus
17	chr2:9876200-9878600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr2:9876400-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:9876800-9878600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:9877000-9879000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:9877000-9879200	Enhancers	Fetal Muscle Leg	muscle
22	chr2:9877200-9877800	Enhancers	Fetal Muscle Trunk	muscle
23	chr2:9877400-9878000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:9877400-9878800	Weak transcription	Thymus	Thymus
25	chr2:9877400-9885000	Weak transcription	HMEC	breast
26	chr2:9877600-9878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:9877600-9878800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:9877600-9879000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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