Variant report

Variant	rs309906
Chromosome Location	chr5:42985370-42985371
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42982424..42987523-chr5:43005404..43009945,6	MCF-7	breast:
2	chr5:42924589..42926644-chr5:42983759..42986055,2	MCF-7	breast:
3	chr5:42984356..42986139-chr5:43039157..43041117,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C5orf39-2	chr5:42985140-42985764	XLOC_004803

Variant related genes	Relation type
ENSG00000271788	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1001717	0.91[JPT][hapmap]
rs10064089	0.94[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12653864	1.00[JPT][hapmap]
rs12654798	1.00[JPT][hapmap]
rs12659721	0.91[JPT][hapmap]
rs13163892	0.91[JPT][hapmap]
rs13164183	0.91[JPT][hapmap]
rs13171253	0.91[JPT][hapmap]
rs16873177	0.91[JPT][hapmap]
rs17242731	0.91[JPT][hapmap]
rs17242995	0.90[JPT][hapmap]
rs17243023	0.91[JPT][hapmap]
rs17243086	0.91[JPT][hapmap]
rs17243165	0.90[JPT][hapmap]
rs17302596	0.91[JPT][hapmap]
rs186322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291632	0.90[JPT][hapmap]
rs2432096	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2548351	0.88[ASN][1000 genomes]
rs309908	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35397154	0.91[JPT][hapmap]
rs3752831	0.91[JPT][hapmap]
rs3752832	0.90[JPT][hapmap]
rs3797306	0.91[JPT][hapmap]
rs3797307	0.91[JPT][hapmap]
rs3797308	0.91[JPT][hapmap]
rs3797309	0.91[JPT][hapmap]
rs585302	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs66521413	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
9	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
12	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
13	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
14	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
15	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
16	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
17	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42967000-42985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:42969400-42985400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr5:42970800-42988400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:42971000-42985400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:42973200-42985600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:42975200-42987600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:42982200-42986000	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr5:42982200-42988000	Enhancers	HUVEC	blood vessel
9	chr5:42982400-42985400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:42982400-42986600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:42982800-42985400	Weak transcription	HSMMtube	muscle
12	chr5:42982800-42987600	Weak transcription	Dnd41	blood
13	chr5:42982800-42989400	Weak transcription	Adipose Nuclei	Adipose
14	chr5:42982800-42990800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:42983000-42985600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:42983000-42990000	Weak transcription	Fetal Thymus	thymus
17	chr5:42983200-42986000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:42983200-42986200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:42983600-42987000	Enhancers	NHEK	skin
20	chr5:42983800-42987000	Enhancers	HMEC	breast
21	chr5:42984000-42986600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:42984400-42985400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:42984400-42985400	Enhancers	NHDF-Ad	bronchial
24	chr5:42984400-42985800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr5:42984400-42985800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr5:42984400-42985800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:42984400-42985800	Enhancers	HSMM	muscle
28	chr5:42984400-42986200	Strong transcription	Primary B cells from cord blood	blood
29	chr5:42984400-42986400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr5:42984400-42986400	Enhancers	A549	lung
31	chr5:42984400-42986400	Enhancers	NH-A	brain
32	chr5:42984400-42986600	Enhancers	Hela-S3	cervix
33	chr5:42984400-42986600	Enhancers	Osteobl	bone
34	chr5:42984400-42986800	Enhancers	NHLF	lung
35	chr5:42984400-42988600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:42984400-42989400	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr5:42984600-42986200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:42985000-42985600	ZNF genes & repeats	K562	blood
39	chr5:42985000-42986200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:42985000-42986200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:42985000-42986400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr5:42985000-42987200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:42985200-42985400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:42985200-42985400	Bivalent Enhancer	Fetal Intestine Large	intestine
45	chr5:42985200-42985400	ZNF genes & repeats	Thymus	Thymus
46	chr5:42985200-42985600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:42985200-42986200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:42985200-42986200	Strong transcription	Primary T cells from cord blood	blood
49	chr5:42985200-42986200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr5:42985200-42986400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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