Variant report

Variant	rs26609
Chromosome Location	chr5:53431896-53431897
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:53430922..53432920-chr5:53605209..53608004,3	K562	blood:
2	chr5:53429696..53432920-chr5:53605209..53609197,3	K562	blood:
3	chr5:53425532..53428018-chr5:53431677..53433643,2	K562	blood:

Variant related genes	Relation type
ENSG00000185305	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10051537	0.86[CHB][hapmap]
rs1345815	0.86[CHB][hapmap]
rs154020	0.94[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs154041	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs156825	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs156827	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs156830	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs157069	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs157072	0.97[ASN][1000 genomes]
rs157073	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1644818	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs165942	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16882414	0.86[CHB][hapmap]
rs202168	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2407404	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs244643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2547538	0.93[CHB][hapmap]
rs25853	0.80[ASN][1000 genomes]
rs26608	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs26610	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs26775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26776	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs277320	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277321	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277323	0.89[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277325	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277327	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277328	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277329	0.89[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277330	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27776	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278065	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs278066	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs279743	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs279744	0.93[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs28033	0.93[CHB][hapmap];0.90[CHD][hapmap]
rs35006	0.93[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs35545340	0.84[ASN][1000 genomes]
rs3797255	0.86[CHB][hapmap]
rs3843452	0.93[CHB][hapmap]
rs464888	0.94[CEU][hapmap];0.93[CHB][hapmap]
rs4865808	0.93[CHB][hapmap]
rs4865809	0.93[CHB][hapmap];0.84[MEX][hapmap]
rs586405	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs682103	0.93[CHB][hapmap];0.84[CHD][hapmap]
rs6866862	0.80[CEU][hapmap];0.93[CHB][hapmap]
rs6866870	0.86[CHB][hapmap]
rs700911	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs700915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
7	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
11	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
14	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1015340	chr5:53326385-53471882	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
18	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
19	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
20	nsv881056	chr5:53368869-53744849	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
21	nsv881408	chr5:53386267-53815495	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv4830	chr5:53420470-53441607	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs26609	NDUFS4	cis	parietal	SCAN
rs26609	SLC38A9	cis	cerebellum	SCAN
rs26609	HSPB3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53409200-53448000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:53409200-53465600	Weak transcription	Fetal Intestine Large	intestine
3	chr5:53409600-53441200	Weak transcription	Primary B cells from cord blood	blood
4	chr5:53424400-53433000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:53425400-53467200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:53426600-53442400	Weak transcription	Left Ventricle	heart
7	chr5:53428000-53471600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:53429400-53433000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:53429400-53455800	Weak transcription	Fetal Intestine Small	intestine
10	chr5:53429600-53432800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:53429600-53434000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:53429800-53432400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:53430000-53446600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr5:53430200-53445400	Weak transcription	K562	blood
15	chr5:53430600-53441200	Weak transcription	Primary T cells from cord blood	blood
16	chr5:53430800-53432800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:53430800-53433200	Enhancers	Fetal Stomach	stomach
18	chr5:53430800-53433400	Enhancers	Colon Smooth Muscle	Colon
19	chr5:53431000-53433000	Weak transcription	Right Atrium	heart
20	chr5:53431200-53433200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:53431400-53432600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:53431600-53432000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr5:53431800-53432800	Weak transcription	Fetal Lung	lung
24	chr5:53431800-53432800	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:53431800-53433000	Weak transcription	NHDF-Ad	bronchial
26	chr5:53431800-53433200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:53431800-53436800	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr5:53431800-53474000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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