Variant report

Variant	rs2597180
Chromosome Location	chr17:46061412-46061413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46053682..46056585-chr17:46059998..46062709,2	K562	blood:
2	chr17:46059948..46063060-chr17:46063175..46066138,4	MCF-7	breast:
3	chr17:46058631..46063478-chr17:46064617..46070061,8	K562	blood:
4	chr17:46046877..46049388-chr17:46060915..46063110,2	K562	blood:
5	chr17:46058567..46062223-chr17:46094441..46097254,3	K562	blood:
6	chr17:46059865..46061717-chr17:46063064..46066103,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1476578	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1476579	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003477	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2003478	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2255697	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255815	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2525084	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525085	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525087	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525088	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525090	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525092	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525093	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525094	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525096	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2525098	0.96[ASN][1000 genomes]
rs2597161	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597165	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597168	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597171	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597172	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597173	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597174	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597179	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597181	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2875746	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905845	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2905846	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905848	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905849	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905850	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905851	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905852	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2905853	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34190379	0.93[ASN][1000 genomes]
rs35653190	0.82[ASN][1000 genomes]
rs62064873	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6503949	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729785	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729786	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs737130	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs739853	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7406338	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7503584	0.93[ASN][1000 genomes]
rs8076314	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs885634	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
2	chr17:46050200-46061800	Strong transcription	NHLF	lung
3	chr17:46050200-46062000	Strong transcription	NHEK	skin
4	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
8	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr17:46050800-46061600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:46050800-46061600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:46050800-46061800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:46050800-46062000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:46050800-46062000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr17:46050800-46062200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr17:46050800-46062400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr17:46050800-46062600	Strong transcription	Fetal Intestine Small	intestine
22	chr17:46050800-46062800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:46050800-46063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr17:46050800-46063000	Strong transcription	Fetal Muscle Leg	muscle
25	chr17:46051000-46061800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr17:46051000-46062000	Strong transcription	Primary B cells from cord blood	blood
27	chr17:46051000-46062200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:46051000-46062200	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr17:46051000-46063000	Strong transcription	Primary T cells from cord blood	blood
30	chr17:46051000-46063000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr17:46051200-46062000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr17:46051800-46062400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr17:46054200-46063000	Strong transcription	Thymus	Thymus
34	chr17:46054600-46061800	Strong transcription	Pancreas	Pancrea
35	chr17:46056200-46064000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:46056400-46061800	Strong transcription	GM12878-XiMat	blood
37	chr17:46056400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:46056400-46063200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:46056600-46061600	Strong transcription	Fetal Brain Female	brain
40	chr17:46056600-46061800	Genic enhancers	K562	blood
41	chr17:46056800-46061800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr17:46057000-46064000	Weak transcription	Fetal Brain Male	brain
43	chr17:46057800-46061800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr17:46057800-46062000	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr17:46058200-46064400	Weak transcription	Fetal Kidney	kidney
46	chr17:46058400-46061800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr17:46058400-46062000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:46059000-46064600	Weak transcription	NHDF-Ad	bronchial
49	chr17:46059200-46061800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr17:46059400-46061800	Enhancers	Right Atrium	heart

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