Variant report

Variant	rs2329713
Chromosome Location	chr21:45642057-45642058
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45620304..45623490-chr21:45641507..45643992,3	MCF-7	breast:
2	chr21:45633515..45635419-chr21:45641635..45644619,2	MCF-7	breast:
3	chr21:45641049..45643518-chr21:45653800..45656237,3	MCF-7	breast:
4	chr21:45641080..45643461-chr21:45659790..45661688,2	MCF-7	breast:
5	chr21:45591261..45594431-chr21:45640713..45642664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000232124	Chromatin interaction
ENSG00000267913	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2298565	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329714	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329716	0.81[AMR][1000 genomes]
rs4511811	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4818890	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4819387	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7280525	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9977351	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv913905	chr21:45640629-45696025	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2329713	ICOSLG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

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	chr21:45632800-45646200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:45637600-45646400	Weak transcription	Gastric	stomach
6	chr21:45638800-45643000	Weak transcription	HMEC	breast
7	chr21:45638800-45649000	Weak transcription	Right Ventricle	heart
8	chr21:45639000-45648600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr21:45639200-45643000	Weak transcription	Esophagus	oesophagus
10	chr21:45639200-45647400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr21:45639200-45647800	Weak transcription	Colonic Mucosa	Colon
12	chr21:45639400-45643000	Weak transcription	Stomach Mucosa	stomach
13	chr21:45639400-45643600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:45639600-45643200	Weak transcription	Hela-S3	cervix
15	chr21:45639600-45648200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr21:45639800-45642800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr21:45639800-45643000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr21:45639800-45643200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:45639800-45659400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr21:45640000-45643000	Weak transcription	Fetal Heart	heart
21	chr21:45640000-45646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr21:45640000-45648400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr21:45640000-45648800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr21:45640000-45659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr21:45640200-45642600	Weak transcription	Fetal Intestine Large	intestine
26	chr21:45640200-45642800	Weak transcription	Fetal Intestine Small	intestine
27	chr21:45640200-45643000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr21:45640200-45648400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr21:45640400-45643000	Weak transcription	Adipose Nuclei	Adipose
30	chr21:45640400-45646200	Weak transcription	Spleen	Spleen
31	chr21:45640600-45643000	Weak transcription	Brain Hippocampus Middle	brain
32	chr21:45640600-45643200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr21:45640600-45646200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr21:45640600-45646400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr21:45640600-45647600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr21:45640600-45653400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr21:45640800-45643000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr21:45641000-45646200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr21:45641200-45643000	Weak transcription	Placenta	Placenta
40	chr21:45641200-45646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr21:45641200-45646600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr21:45641200-45648000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr21:45641200-45648200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr21:45641400-45643000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:45641400-45643600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr21:45641600-45643200	Weak transcription	GM12878-XiMat	blood
47	chr21:45641600-45654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr21:45642000-45642400	Weak transcription	Primary B cells from cord blood	blood
49	chr21:45642000-45643600	Enhancers	Primary B cells from peripheral blood	blood

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