Variant report

Variant	rs2597165
Chromosome Location	chr17:46070706-46070707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46065135..46066794-chr17:46070523..46072914,2	MCF-7	breast:
2	chr17:46070058..46071807-chr17:46072298..46074102,2	K562	blood:
3	chr17:45898759..45901356-chr17:46070132..46072783,2	MCF-7	breast:
4	chr17:46070659..46072225-chr17:46102465..46104720,2	K562	blood:
5	chr17:46070411..46072962-chr17:46123437..46126106,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082641	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000264701	Chromatin interaction
ENSG00000006025	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11545723	0.82[CHB][hapmap]
rs1476578	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476579	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003477	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003478	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2255697	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255815	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2525084	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2525085	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525087	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525088	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525090	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525091	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525092	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525093	0.88[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525094	1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525096	0.95[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525098	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2597161	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597166	0.91[AFR][1000 genomes]
rs2597168	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597171	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597172	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597173	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597174	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597179	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597180	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2597181	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2875746	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905845	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2905846	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905848	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905849	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905850	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905851	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905852	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905853	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34190379	0.92[ASN][1000 genomes]
rs35653190	0.85[ASN][1000 genomes]
rs4793734	0.82[CHB][hapmap]
rs62064873	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503949	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729786	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737130	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs739853	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7406338	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7503584	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs8076314	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs885634	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
2	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
3	nsv527427	chr17:46070253-46071584	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2597165	HOXB2	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46061800-46079600	Weak transcription	Right Atrium	heart
2	chr17:46063400-46074200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:46063600-46074600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:46064200-46071000	Enhancers	HSMMtube	muscle
5	chr17:46064800-46071400	Weak transcription	Pancreas	Pancrea
6	chr17:46065400-46072600	Weak transcription	Fetal Lung	lung
7	chr17:46066400-46072600	Weak transcription	Spleen	Spleen
8	chr17:46068000-46070800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:46068000-46074200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:46068000-46079800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr17:46068200-46071000	Enhancers	Fetal Brain Female	brain
12	chr17:46068200-46074200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:46068400-46073000	Weak transcription	Fetal Kidney	kidney
14	chr17:46069000-46071600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:46069000-46071600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:46069000-46072200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:46069000-46072600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:46069000-46077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr17:46069000-46079600	Weak transcription	Fetal Thymus	thymus
20	chr17:46069200-46072000	Weak transcription	Brain Germinal Matrix	brain
21	chr17:46069200-46072000	Weak transcription	Fetal Brain Male	brain
22	chr17:46069200-46074400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:46069400-46072000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr17:46069400-46072000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr17:46069400-46072600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:46069400-46072600	Weak transcription	Fetal Muscle Leg	muscle
27	chr17:46069600-46070800	Enhancers	Right Ventricle	heart
28	chr17:46069600-46071800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:46069800-46071600	Weak transcription	Placenta	Placenta
30	chr17:46069800-46071800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr17:46069800-46074400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:46069800-46075000	Weak transcription	HSMM	muscle
33	chr17:46070000-46071600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr17:46070000-46071600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr17:46070000-46071600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:46070000-46072000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr17:46070000-46072200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr17:46070000-46073000	Weak transcription	K562	blood
39	chr17:46070000-46075000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:46070200-46072000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr17:46070600-46070800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr17:46070600-46071600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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