Variant report

Variant	rs229341
Chromosome Location	chr21:44889292-44889293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:44887407..44890768-chr21:44921075..44924362,4	MCF-7	breast:
2	chr21:44887736..44889774-chr21:44897882..44899810,2	MCF-7	breast:
3	chr21:44883686..44886914-chr21:44887585..44890548,3	K562	blood:
4	chr21:44886960..44890249-chr21:44891920..44896303,5	MCF-7	breast:
5	chr21:44864853..44867351-chr21:44888801..44891094,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223975	Chromatin interaction
ENSG00000185186	Chromatin interaction
ENSG00000188660	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1378079	0.86[CHD][hapmap]
rs162367	0.83[CHD][hapmap]
rs162378	0.83[CHD][hapmap]
rs2838320	0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2838336	0.83[CHD][hapmap]
rs2838338	0.83[CHD][hapmap]
rs2838341	0.83[CHD][hapmap]
rs389278	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs4818858	0.96[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913831	chr21:44563995-44931821	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv913838	chr21:44740134-44931821	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
5	nsv913839	chr21:44750200-44931821	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
6	nsv913847	chr21:44792003-44931821	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
7	nsv913849	chr21:44817248-44925334	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
8	nsv913852	chr21:44829087-44925334	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
9	nsv913860	chr21:44831981-44925334	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS 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	95 gene(s)	inside rSNPs	diseases
10	nsv913867	chr21:44835508-44925334	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	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
12	nsv913872	chr21:44860542-44925334	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv1061369	chr21:44886596-44931388	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv544468	chr21:44886596-44931388	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229341	TMPRSS2	cis	parietal	SCAN
rs229341	HSF2BP	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44879400-44889400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr21:44880600-44890800	Enhancers	HepG2	liver
3	chr21:44882600-44891200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr21:44883400-44889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr21:44884000-44891000	Weak transcription	Psoas Muscle	Psoas
6	chr21:44884800-44890800	Weak transcription	Fetal Stomach	stomach
7	chr21:44885600-44894000	Weak transcription	Hela-S3	cervix
8	chr21:44887400-44889400	Weak transcription	HSMM	muscle
9	chr21:44887600-44891600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr21:44887800-44889800	Weak transcription	NH-A	brain
11	chr21:44887800-44890600	Enhancers	Fetal Intestine Small	intestine
12	chr21:44888000-44889600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr21:44888000-44890400	Weak transcription	Lung	lung
14	chr21:44888000-44891800	Enhancers	Fetal Intestine Large	intestine
15	chr21:44888000-44894000	Weak transcription	A549	lung
16	chr21:44888000-44897200	Weak transcription	HUVEC	blood vessel
17	chr21:44888200-44890000	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr21:44888200-44890200	Enhancers	Stomach Mucosa	stomach
19	chr21:44888200-44892600	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr21:44888400-44891200	Weak transcription	Right Atrium	heart
21	chr21:44888400-44892000	Weak transcription	Fetal Kidney	kidney
22	chr21:44888600-44889800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr21:44888600-44891400	Weak transcription	Fetal Lung	lung
24	chr21:44888600-44891400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr21:44888800-44890200	Enhancers	HSMMtube	muscle
26	chr21:44888800-44891200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr21:44889000-44890200	Enhancers	Spleen	Spleen
28	chr21:44889000-44891200	Enhancers	Esophagus	oesophagus
29	chr21:44889000-44891400	Enhancers	Fetal Muscle Leg	muscle
30	chr21:44889000-44897000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr21:44889200-44890000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr21:44889200-44890400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr21:44889200-44890400	Weak transcription	Gastric	stomach
34	chr21:44889200-44890600	Enhancers	Duodenum Mucosa	Duodenum

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