Variant report

Variant	rs162396
Chromosome Location	chr21:44947807-44947808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44947794..44949507-chr21:44953072..44955279,2	K562	blood:
2	chr21:44947553..44949798-chr21:44957726..44959833,2	MCF-7	breast:
3	chr21:44935610..44937483-chr21:44946827..44948859,2	MCF-7	breast:

Extended variants
information (count: 143 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1003280	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1073522	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs11089020	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1122873	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs11701518	0.87[YRI][hapmap]
rs11701673	0.84[EUR][1000 genomes]
rs12626757	0.93[ASN][1000 genomes]
rs12627667	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap]
rs1378079	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378080	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs141521	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1454648	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs1454650	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs1454651	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.93[ASN][1000 genomes]
rs1584917	0.85[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs1584918	0.85[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs1598206	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs162343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162344	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162345	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162366	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs162367	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162368	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162369	0.95[ASN][1000 genomes]
rs162371	0.82[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs162372	0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162373	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162374	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162375	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162376	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162377	0.86[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs162378	0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs162379	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs162380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs162381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs162388	0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs162389	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs162390	1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs162391	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162392	0.83[ASN][1000 genomes]
rs162393	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162394	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162395	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162400	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162401	0.92[EUR][1000 genomes]
rs162402	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs162403	0.96[ASN][1000 genomes]
rs162404	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs167930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1836854	0.82[AMR][1000 genomes]
rs1836855	0.81[AMR][1000 genomes]
rs1836856	0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs189094	0.95[ASN][1000 genomes]
rs2246602	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs229340	0.82[ASN][1000 genomes]
rs229357	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs230640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs230641	0.84[EUR][1000 genomes]
rs230642	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs230643	0.96[ASN][1000 genomes]
rs230644	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs230645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs230646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs230647	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2329442	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2329443	0.81[ASN][1000 genomes]
rs2838316	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2838317	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838318	0.96[CEU][hapmap]
rs2838319	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838320	0.84[CEU][hapmap]
rs2838321	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838322	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838323	0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838324	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2838325	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2838326	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2838328	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838329	0.94[ASN][1000 genomes]
rs2838330	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2838331	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2838336	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs2838337	0.86[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs2838338	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2838339	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2838340	0.92[CEU][hapmap]
rs2838341	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.89[YRI][hapmap]
rs2838343	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[YRI][hapmap]
rs28840140	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3788062	0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs463738	0.96[ASN][1000 genomes]
rs4818833	0.87[ASN][1000 genomes]
rs4818843	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4818850	0.93[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4818856	0.92[ASN][1000 genomes]
rs4819264	0.92[ASN][1000 genomes]
rs4819270	0.85[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs4997353	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56369437	0.82[AMR][1000 genomes]
rs6518301	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6518302	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs6518309	0.86[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6518310	0.82[CEU][hapmap]
rs7275705	0.82[ASN][1000 genomes]
rs7276215	0.89[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs7276316	0.87[ASN][1000 genomes]
rs7276633	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[YRI][hapmap]
rs7277539	0.84[CEU][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7279958	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7279968	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap]
rs7282933	0.92[ASN][1000 genomes]
rs7283362	0.89[YRI][hapmap]
rs8129601	0.81[CEU][hapmap]
rs8131005	0.93[CEU][hapmap]
rs8131020	0.89[YRI][hapmap]
rs8131027	0.82[CEU][hapmap]
rs8133523	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap]
rs86138	0.95[ASN][1000 genomes]
rs86139	0.82[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs91424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs9306159	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9974710	0.81[ASN][1000 genomes]
rs9976441	0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9978811	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9980185	0.91[CEU][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs9981291	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs9981790	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9983763	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs9984002	0.87[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057726	chr21:44711850-44957303	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	117 gene(s)	inside rSNPs	diseases
2	nsv544466	chr21:44711850-44957303	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv913868	chr21:44835508-44954522	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS 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	98 gene(s)	inside rSNPs	diseases
4	esv1839560	chr21:44864079-44973184	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
5	nsv913873	chr21:44879869-45142427	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv587689	chr21:44884252-44986050	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv1061539	chr21:44915533-45041824	Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1067171	chr21:44921187-45039471	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
9	nsv521700	chr21:44925334-45041790	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv470903	chr21:44925334-45061501	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv459289	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
12	nsv587690	chr21:44925334-45064600	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs162396	HSF2BP	cis	multi-tissue	Pritchard
rs162396	HSF2BP	cis	Lymphoblastoid	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44941000-44949400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr21:44943000-44949400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr21:44943400-44949000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:44943400-44956800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr21:44943600-44952400	Weak transcription	HMEC	breast
6	chr21:44943600-44952600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:44945400-44948800	Enhancers	Fetal Brain Male	brain
8	chr21:44945400-44949600	Strong transcription	HSMMtube	muscle
9	chr21:44945600-44951400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr21:44946800-44951600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr21:44946800-44962800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr21:44947600-44949800	Strong transcription	NHEK	skin
13	chr21:44947800-44948000	Flanking Active TSS	Fetal Brain Female	brain
14	chr21:44947800-44949600	Strong transcription	HSMM	muscle

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