Variant report

Variant	rs17593
Chromosome Location	chr15:42680058-42680059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42679543..42681444-chr15:42683292..42685260,2	K562	blood:
2	chr15:42678390..42681163-chr15:42692112..42694875,2	K562	blood:
3	chr15:42679521..42681202-chr15:42684595..42687043,2	MCF-7	breast:
4	chr15:42559733..42563310-chr15:42678634..42681534,3	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12441027	1.00[MEX][hapmap]
rs1678998	1.00[MEX][hapmap]
rs16972927	0.83[EUR][1000 genomes]
rs16972930	0.83[EUR][1000 genomes]
rs16972969	0.83[EUR][1000 genomes]
rs16973015	1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs16973018	0.83[EUR][1000 genomes]
rs16973022	0.83[EUR][1000 genomes]
rs16973177	1.00[EUR][1000 genomes]
rs16973182	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973184	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973188	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973200	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16973206	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16973233	1.00[MEX][hapmap]
rs2412694	1.00[MEX][hapmap]
rs2412697	1.00[MEX][hapmap]
rs28364383	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28364385	0.91[AFR][1000 genomes]
rs28364387	0.83[EUR][1000 genomes]
rs28364395	1.00[MEX][hapmap]
rs28364396	1.00[MEX][hapmap]
rs28364399	0.87[ASW][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28364407	1.00[MEX][hapmap]
rs28364423	1.00[GIH][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs28364432	1.00[MEX][hapmap]
rs28364443	1.00[MEX][hapmap]
rs28364485	1.00[MEX][hapmap]
rs28364496	1.00[MEX][hapmap]
rs28364534	1.00[MEX][hapmap]
rs4307925	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4486855	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4516202	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4923941	1.00[MEX][hapmap]
rs4924650	1.00[MEX][hapmap]
rs4924668	1.00[MEX][hapmap]
rs4924669	1.00[MEX][hapmap]
rs4924671	1.00[MEX][hapmap]
rs5029919	0.86[EUR][1000 genomes]
rs7167683	1.00[ASW][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7174880	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176832	1.00[MEX][hapmap]
rs728507	1.00[EUR][1000 genomes]
rs728508	1.00[EUR][1000 genomes]
rs728509	1.00[EUR][1000 genomes]
rs728510	0.83[EUR][1000 genomes]
rs8024452	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8026890	1.00[EUR][1000 genomes]
rs8027800	1.00[EUR][1000 genomes]
rs8033108	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8033734	1.00[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8033882	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8033960	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8035332	1.00[EUR][1000 genomes]
rs8035521	1.00[EUR][1000 genomes]
rs8037627	1.00[MEX][hapmap]
rs8038771	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038967	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039470	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040129	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040726	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs934877	0.83[EUR][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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42652800-42684400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:42672400-42688800	Weak transcription	Esophagus	oesophagus
7	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
8	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:42674600-42682600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:42674600-42684400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:42675200-42683600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:42675200-42684800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:42675600-42691600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:42676200-42682400	Strong transcription	Liver	Liver
16	chr15:42676400-42680600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:42676600-42680200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:42676800-42680200	Genic enhancers	Fetal Muscle Leg	muscle
19	chr15:42676800-42680400	Strong transcription	Primary B cells from cord blood	blood
20	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
21	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood
22	chr15:42677200-42684000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:42677400-42687800	Weak transcription	Brain Substantia Nigra	brain
24	chr15:42677600-42689000	Weak transcription	Right Ventricle	heart
25	chr15:42677800-42680200	Enhancers	HSMMtube	muscle
26	chr15:42677800-42682600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:42678200-42680200	Strong transcription	Aorta	Aorta
28	chr15:42678200-42680200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:42678200-42688000	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:42678400-42680200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr15:42678400-42681600	Weak transcription	HepG2	liver
32	chr15:42678400-42682200	Weak transcription	Fetal Intestine Large	intestine
33	chr15:42678400-42687400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:42678600-42691200	Weak transcription	Gastric	stomach
35	chr15:42678600-42706800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:42678800-42684600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:42678800-42691600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr15:42678800-42694000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:42678800-42702800	Weak transcription	NHLF	lung
40	chr15:42679000-42681000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr15:42679000-42681200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr15:42679000-42683600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:42679000-42684400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:42679000-42687400	Weak transcription	Spleen	Spleen
45	chr15:42679000-42691400	Weak transcription	Thymus	Thymus
46	chr15:42679000-42706800	Weak transcription	Right Atrium	heart
47	chr15:42679200-42680400	Enhancers	Lung	lung
48	chr15:42679200-42681000	Weak transcription	Ovary	ovary
49	chr15:42679200-42681200	Weak transcription	Psoas Muscle	Psoas
50	chr15:42679200-42681400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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