Variant report

Variant	rs162379
Chromosome Location	chr21:44925334-44925335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:44920414..44926751-chr21:45027970..45034874,9	MCF-7	breast:
2	chr21:44826611..44829527-chr21:44923973..44926200,2	MCF-7	breast:
3	chr21:44839515..44855046-chr21:44918803..44938582,70	MCF-7	breast:
4	chr21:44924498..44927329-chr21:45064955..45067005,2	MCF-7	breast:
5	chr21:44896492..44901028-chr21:44922063..44925806,9	MCF-7	breast:
6	chr21:44903235..44910338-chr21:44918042..44927375,22	MCF-7	breast:
7	chr21:44924283..44926867-chr21:45004236..45006835,2	MCF-7	breast:
8	chr21:44923746..44926037-chr21:44940122..44942028,2	K562	blood:
9	chr21:44766255..44769691-chr21:44923906..44926026,3	MCF-7	breast:
10	chr21:44760916..44764900-chr21:44922061..44925479,7	MCF-7	breast:
11	chr21:44922977..44925347-chr21:45002345..45004091,2	MCF-7	breast:
12	chr21:44760657..44765448-chr21:44921066..44925837,8	MCF-7	breast:
13	chr21:44841823..44851058-chr21:44912330..44925700,37	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000142178	Chromatin interaction
ENSG00000185186	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1003280	0.88[CEU][hapmap]
rs1073522	0.81[CEU][hapmap]
rs12627667	0.85[CEU][hapmap]
rs1378079	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs1378080	0.89[CEU][hapmap]
rs141521	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs1598206	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs162343	0.92[CEU][hapmap]
rs162345	0.92[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs162367	0.81[CEU][hapmap]
rs162373	0.83[EUR][1000 genomes]
rs162375	0.85[CEU][hapmap]
rs162376	0.85[CEU][hapmap]
rs162388	0.81[CEU][hapmap]
rs162395	0.84[EUR][1000 genomes]
rs162396	0.84[EUR][1000 genomes]
rs162398	0.92[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs162399	0.85[CEU][hapmap]
rs162400	0.85[CEU][hapmap]
rs162401	0.91[EUR][1000 genomes]
rs167930	0.84[EUR][1000 genomes]
rs229357	0.81[CEU][hapmap]
rs230640	0.86[EUR][1000 genomes]
rs230641	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs230644	0.86[EUR][1000 genomes]
rs230645	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs230646	0.92[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs2838311	0.82[YRI][hapmap]
rs2838317	0.88[CEU][hapmap]
rs2838318	0.89[CEU][hapmap]
rs2838319	0.88[CEU][hapmap]
rs2838321	0.88[CEU][hapmap]
rs2838323	0.88[CEU][hapmap]
rs2838324	0.81[CEU][hapmap]
rs2838325	0.85[CEU][hapmap];0.98[TSI][hapmap]
rs2838326	0.85[CEU][hapmap];0.98[TSI][hapmap]
rs2838328	0.85[CEU][hapmap]
rs2838330	0.85[CEU][hapmap]
rs2838334	0.91[YRI][hapmap]
rs2838336	0.85[CEU][hapmap]
rs2838340	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs2838341	0.85[CEU][hapmap]
rs2838343	0.85[CEU][hapmap]
rs4818850	0.85[CEU][hapmap]
rs6518301	0.85[CEU][hapmap]
rs7276215	0.81[CEU][hapmap]
rs7276633	0.81[CEU][hapmap]
rs7279958	0.85[CEU][hapmap]
rs7279968	0.85[CEU][hapmap]
rs7283362	0.82[TSI][hapmap]
rs8131005	0.85[CEU][hapmap]
rs8133780	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs9976441	0.85[CEU][hapmap]
rs9978811	0.87[CEU][hapmap]
rs9980185	0.83[CEU][hapmap]
rs9981790	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 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
18	nsv1059264	chr21:44895863-44944515	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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
22	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
23	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
24	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs162379	DNMT3L	cis	cerebellum	SCAN
rs162379	HSF2BP	cis	lymphoblastoid	seeQTL
rs162379	NCRNA00175	cis	parietal	SCAN
rs162379	PCNT	cis	cerebellum	SCAN
rs162379	PCP4	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:44918800-44930200	Weak transcription	Fetal Kidney	kidney
2	chr21:44919800-44936800	Weak transcription	Fetal Brain Female	brain
3	chr21:44921800-44926400	Enhancers	Left Ventricle	heart
4	chr21:44922800-44925600	Enhancers	Adipose Nuclei	Adipose
5	chr21:44922800-44926800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr21:44922800-44936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:44923200-44926400	Weak transcription	Fetal Lung	lung
8	chr21:44923400-44926000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr21:44923400-44926000	Weak transcription	Fetal Stomach	stomach
10	chr21:44923400-44926200	Weak transcription	Ovary	ovary
11	chr21:44923400-44926400	Weak transcription	Esophagus	oesophagus
12	chr21:44923400-44926400	Weak transcription	NHEK	skin
13	chr21:44923400-44926600	Weak transcription	Psoas Muscle	Psoas
14	chr21:44923400-44929000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr21:44923400-44934000	Weak transcription	Gastric	stomach
16	chr21:44923400-44936600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:44923400-44936600	Weak transcription	Brain Germinal Matrix	brain
18	chr21:44923600-44926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr21:44924000-44925400	Enhancers	Lung	lung
20	chr21:44924000-44925600	Enhancers	Right Ventricle	heart
21	chr21:44924000-44925800	Weak transcription	HSMM	muscle
22	chr21:44924000-44926000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr21:44924000-44926200	Weak transcription	HepG2	liver
24	chr21:44924000-44926400	Weak transcription	Pancreas	Pancrea
25	chr21:44924000-44926600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr21:44924000-44926600	Weak transcription	Fetal Intestine Large	intestine
27	chr21:44924000-44926600	Weak transcription	Fetal Intestine Small	intestine
28	chr21:44924000-44927200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr21:44924000-44927600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr21:44924000-44930200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr21:44924200-44926200	Weak transcription	Placenta	Placenta
32	chr21:44924200-44929800	Weak transcription	HMEC	breast
33	chr21:44924400-44925400	Enhancers	Right Atrium	heart
34	chr21:44924400-44925400	Strong transcription	HSMMtube	muscle
35	chr21:44924400-44926400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr21:44924400-44926600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr21:44924400-44927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr21:44924400-44929200	Weak transcription	A549	lung
39	chr21:44924600-44925400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr21:44924800-44926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr21:44925200-44925400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr21:44925200-44925600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr21:44925200-44926200	Weak transcription	Placenta Amnion	Placenta Amnion

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