Variant report

Variant	rs2070554
Chromosome Location	chr21:45640139-45640140
allele	G/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45637874..45640737-chr21:45652531..45655334,2	MCF-7	breast:
2	chr21:45637636..45640956-chr21:45661307..45664168,3	MCF-7	breast:
3	chr21:45638620..45641640-chr21:45644035..45648127,5	MCF-7	breast:
4	chr21:45638138..45641604-chr21:45643124..45645379,3	MCF-7	breast:
5	chr21:45631740..45633911-chr21:45635590..45640208,4	MCF-7	breast:
6	chr21:45571719..45574629-chr21:45639760..45641612,2	MCF-7	breast:
7	chr21:45633493..45635981-chr21:45638938..45640638,2	MCF-7	breast:
8	chr21:45638024..45640421-chr21:45658228..45660769,4	MCF-7	breast:
9	chr21:45626500..45630389-chr21:45636831..45640533,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000232698	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1048710	0.80[EUR][1000 genomes]
rs12482807	0.80[EUR][1000 genomes]
rs2838531	0.85[CEU][hapmap]
rs2838532	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2838533	0.81[EUR][1000 genomes]
rs4818887	0.85[CEU][hapmap];0.92[TSI][hapmap]
rs4819388	0.90[TSI][hapmap]
rs6518352	0.90[TSI][hapmap]
rs7276227	0.81[EUR][1000 genomes]
rs7278940	0.90[TSI][hapmap]
rs7283760	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
4	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
5	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
6	nsv913897	chr21:45528919-45640139	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription 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	65 gene(s)	inside rSNPs	diseases
9	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
10	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
11	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
12	nsv913900	chr21:45577102-45640139	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
15	nsv470906	chr21:45627976-45661343	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv587739	chr21:45628374-45640629	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
17	nsv459295	chr21:45629565-45849864	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
18	nsv587740	chr21:45629565-45849864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	57 gene(s)	inside rSNPs	diseases
19	nsv913903	chr21:45630608-45657970	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv913904	chr21:45636881-45700641	Genic enhancers Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2070554	C21orf33	cis	parietal	SCAN
rs2070554	PSMG1	cis	cerebellum	SCAN
rs2070554	ICOSLG	Cis_1M	lymphoblastoid	RTeQTL
rs2070554	TRPM2	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45628600-45659600	Weak transcription	Right Atrium	heart
2	chr21:45628800-45646800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr21:45632200-45659600	Weak transcription	Fetal Kidney	kidney
4	chr21:45632800-45640400	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr21:45632800-45646200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr21:45636200-45640600	Enhancers	Fetal Muscle Leg	muscle
7	chr21:45637200-45642000	Enhancers	Primary B cells from cord blood	blood
8	chr21:45637400-45640200	Enhancers	Fetal Intestine Small	intestine
9	chr21:45637600-45641200	Enhancers	Duodenum Mucosa	Duodenum
10	chr21:45637600-45641600	Enhancers	Primary B cells from peripheral blood	blood
11	chr21:45637600-45646400	Weak transcription	Gastric	stomach
12	chr21:45637800-45640200	Enhancers	Fetal Intestine Large	intestine
13	chr21:45637800-45641400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr21:45637800-45641400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr21:45638000-45640600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:45638000-45640600	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr21:45638200-45640600	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr21:45638200-45640600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr21:45638200-45641200	Enhancers	Placenta	Placenta
20	chr21:45638400-45640200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr21:45638400-45640200	Enhancers	Placenta Amnion	Placenta Amnion
22	chr21:45638400-45640800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr21:45638600-45641200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr21:45638800-45640200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr21:45638800-45643000	Weak transcription	HMEC	breast
26	chr21:45638800-45649000	Weak transcription	Right Ventricle	heart
27	chr21:45639000-45648600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr21:45639200-45640200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr21:45639200-45643000	Weak transcription	Esophagus	oesophagus
30	chr21:45639200-45647400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr21:45639200-45647800	Weak transcription	Colonic Mucosa	Colon
32	chr21:45639400-45640200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr21:45639400-45640400	Enhancers	Adipose Nuclei	Adipose
34	chr21:45639400-45640600	Enhancers	Brain Hippocampus Middle	brain
35	chr21:45639400-45643000	Weak transcription	Stomach Mucosa	stomach
36	chr21:45639400-45643600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr21:45639600-45640400	Enhancers	Spleen	Spleen
38	chr21:45639600-45640400	Flanking Active TSS	GM12878-XiMat	blood
39	chr21:45639600-45640600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr21:45639600-45643200	Weak transcription	Hela-S3	cervix
41	chr21:45639600-45648200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr21:45639800-45641200	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr21:45639800-45642800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr21:45639800-45643000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr21:45639800-45643200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr21:45639800-45659400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr21:45640000-45640200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr21:45640000-45640200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr21:45640000-45640600	Enhancers	Primary hematopoietic stem cells	blood
50	chr21:45640000-45641000	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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