Variant report

Variant	rs7277998
Chromosome Location	chr21:45504523-45504524
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:45504401-45504571	K562	blood:	n/a	n/a
2	POLR2A	chr21:45504419-45505190	K562	blood:	n/a	n/a
3	POLR2A	chr21:45504446-45505620	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45502612..45504623-chr21:45528880..45531046,2	K562	blood:
2	chr21:45503327..45504918-chr21:45507746..45509670,2	MCF-7	breast:
3	chr21:45430699..45434515-chr21:45503432..45505385,3	MCF-7	breast:

Variant related genes	Relation type
TRAPPC10	TF binding region
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17004622	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs34694890	1.00[AMR][1000 genomes]
rs57937156	1.00[AMR][1000 genomes]
rs59292357	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59464702	1.00[AMR][1000 genomes]
rs60541190	1.00[AMR][1000 genomes]
rs7275604	0.82[YRI][hapmap]
rs7277785	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers 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	39 gene(s)	inside rSNPs	diseases
4	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv913890	chr21:45482950-45603746	Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv459294	chr21:45499171-45595060	Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv587722	chr21:45499171-45595060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45445400-45509400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr21:45473000-45526600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr21:45481600-45510800	Strong transcription	Dnd41	blood
4	chr21:45481600-45523800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr21:45485800-45506800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr21:45485800-45506800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:45486200-45524000	Strong transcription	GM12878-XiMat	blood
8	chr21:45488400-45523800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:45488600-45507200	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr21:45489000-45504600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr21:45491200-45510800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr21:45491400-45514600	Strong transcription	Osteobl	bone
13	chr21:45491600-45514600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr21:45492600-45510800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:45493000-45508400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr21:45493000-45510400	Strong transcription	HSMM	muscle
17	chr21:45493000-45510800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr21:45493400-45514800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:45493600-45510800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr21:45493600-45510800	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr21:45493600-45515000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr21:45493800-45514400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr21:45494000-45510800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr21:45495000-45507800	Weak transcription	Fetal Brain Male	brain
25	chr21:45495600-45526800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr21:45496200-45510800	Strong transcription	Fetal Brain Female	brain
27	chr21:45496200-45514200	Strong transcription	Brain Germinal Matrix	brain
28	chr21:45496200-45514600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr21:45497000-45510000	Weak transcription	Psoas Muscle	Psoas
30	chr21:45497200-45506800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr21:45497400-45514600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr21:45498000-45512400	Strong transcription	HMEC	breast
33	chr21:45498400-45524000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr21:45498600-45511000	Strong transcription	HepG2	liver
35	chr21:45498600-45512400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr21:45498600-45523800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr21:45498800-45510800	Strong transcription	NH-A	brain
38	chr21:45499000-45523600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr21:45499000-45524000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr21:45499200-45504600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr21:45499600-45504600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr21:45499600-45504800	Strong transcription	NHDF-Ad	bronchial
43	chr21:45499800-45505200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr21:45500000-45507400	Weak transcription	Ovary	ovary
45	chr21:45500000-45507600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr21:45501000-45505000	Strong transcription	Colon Smooth Muscle	Colon
47	chr21:45501000-45505200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr21:45501400-45504800	Genic enhancers	Brain Hippocampus Middle	brain
49	chr21:45501600-45505400	Genic enhancers	Brain Cingulate Gyrus	brain
50	chr21:45501600-45507800	Weak transcription	Small Intestine	intestine

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