Variant report

Variant	rs55878170
Chromosome Location	chr21:47944226-47944227
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47942256..47945215-chr21:47945222..47947997,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202239	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11508685	1.00[ASN][1000 genomes]
rs16979254	1.00[ASN][1000 genomes]
rs1892693	1.00[ASN][1000 genomes]
rs2839219	1.00[ASN][1000 genomes]
rs2839252	1.00[ASN][1000 genomes]
rs2839264	1.00[ASN][1000 genomes]
rs2839266	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839303	1.00[ASN][1000 genomes]
rs2839315	1.00[ASN][1000 genomes]
rs2839316	1.00[ASN][1000 genomes]
rs56034615	1.00[ASN][1000 genomes]
rs7283507	1.00[ASN][1000 genomes]
rs73146739	1.00[ASN][1000 genomes]
rs73148704	1.00[ASN][1000 genomes]
rs73152856	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
2	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
3	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
4	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
5	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
6	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
7	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
9	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
10	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
11	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
12	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
14	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
15	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
16	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
18	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
19	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
20	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
21	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
22	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
23	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
24	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
26	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a
27	nsv587999	chr21:47941916-48103851	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55878170	SPATC1L	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47927400-47950000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:47931800-47953600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr21:47932000-47953400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:47932000-47961400	Weak transcription	Fetal Brain Male	brain
5	chr21:47932200-47954000	Weak transcription	A549	lung
6	chr21:47932400-47947000	Weak transcription	NHDF-Ad	bronchial
7	chr21:47932400-47947600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:47932400-47947600	Weak transcription	Esophagus	oesophagus
9	chr21:47932400-47950000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr21:47932400-47952000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr21:47932400-47952000	Weak transcription	HSMMtube	muscle
12	chr21:47932400-47954400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr21:47932400-47957400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr21:47932600-47952000	Weak transcription	NHLF	lung
15	chr21:47932600-47953400	Weak transcription	Colonic Mucosa	Colon
16	chr21:47932800-47948800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr21:47933000-47967200	Weak transcription	Fetal Kidney	kidney
18	chr21:47933400-47950600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr21:47933600-47949600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr21:47933600-47953400	Weak transcription	Psoas Muscle	Psoas
21	chr21:47933800-47952000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr21:47935200-47952800	Weak transcription	Colon Smooth Muscle	Colon
23	chr21:47935400-47952000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr21:47935400-47953400	Weak transcription	NH-A	brain
25	chr21:47935600-47945000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr21:47935600-47953400	Weak transcription	Brain Anterior Caudate	brain
27	chr21:47935800-47947600	Weak transcription	Right Atrium	heart
28	chr21:47935800-47952000	Weak transcription	Pancreas	Pancrea
29	chr21:47936000-47945600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr21:47936000-47946600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr21:47936200-47946000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr21:47936200-47946200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr21:47937200-47944400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr21:47937600-47953400	Weak transcription	Brain Angular Gyrus	brain
35	chr21:47937800-47946000	Weak transcription	GM12878-XiMat	blood
36	chr21:47937800-47947200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr21:47937800-47952000	Weak transcription	Brain Substantia Nigra	brain
38	chr21:47937800-47953400	Weak transcription	Brain Hippocampus Middle	brain
39	chr21:47937800-47953400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr21:47938000-47947600	Weak transcription	Left Ventricle	heart
41	chr21:47938000-47949000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr21:47938000-47949800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr21:47938000-47950000	Weak transcription	HSMM	muscle
44	chr21:47938000-47952000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr21:47938000-47953800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr21:47938000-47955800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr21:47938200-47950000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr21:47938200-47950600	Weak transcription	Aorta	Aorta
49	chr21:47938400-47945000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr21:47938400-47945200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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