Variant report

Variant	rs2298565
Chromosome Location	chr21:45643396-45643397
allele	C/G
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	chr21:45642545..45644733-chr21:45651214..45653220,2	K562	blood:
6	chr21:45638138..45641604-chr21:45643124..45645379,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000232124	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2329713	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329714	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329716	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2838527	0.85[CEU][hapmap]
rs4511811	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4818890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819387	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277227	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7278004	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7279626	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7280525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8130872	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs8134498	0.82[EUR][1000 genomes]
rs9977351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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
rs2298565	ICOSLG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 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	chr21:45632800-45646200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr21:45637600-45646400	Weak transcription	Gastric	stomach
6	chr21:45638800-45649000	Weak transcription	Right Ventricle	heart
7	chr21:45639000-45648600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr21:45639200-45647400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr21:45639200-45647800	Weak transcription	Colonic Mucosa	Colon
10	chr21:45639400-45643600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr21:45639600-45648200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr21:45639800-45659400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr21:45640000-45646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr21:45640000-45648400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr21:45640000-45648800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr21:45640000-45659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr21:45640200-45648400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr21:45640400-45646200	Weak transcription	Spleen	Spleen
19	chr21:45640600-45646200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr21:45640600-45646400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr21:45640600-45647600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr21:45640600-45653400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr21:45641000-45646200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:45641200-45646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr21:45641200-45646600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr21:45641200-45648000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr21:45641200-45648200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr21:45641400-45643600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr21:45641600-45654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr21:45642000-45643600	Enhancers	Primary B cells from peripheral blood	blood
31	chr21:45642200-45646200	Enhancers	Fetal Muscle Leg	muscle
32	chr21:45642400-45643600	Enhancers	Primary B cells from cord blood	blood
33	chr21:45642600-45643400	Enhancers	Fetal Intestine Large	intestine
34	chr21:45642800-45643600	Enhancers	Brain Cingulate Gyrus	brain
35	chr21:45642800-45643600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr21:45642800-45643600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr21:45642800-45644000	Enhancers	Fetal Intestine Small	intestine
38	chr21:45643000-45643400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr21:45643000-45643400	Enhancers	Esophagus	oesophagus
40	chr21:45643000-45643400	Enhancers	Ovary	ovary
41	chr21:45643000-45643600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr21:45643000-45643600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr21:45643000-45643600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
44	chr21:45643000-45643600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:45643000-45643600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr21:45643000-45643600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr21:45643000-45643600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:45643000-45643600	Enhancers	Adipose Nuclei	Adipose
49	chr21:45643000-45643600	Enhancers	Brain Angular Gyrus	brain
50	chr21:45643000-45643600	Enhancers	Brain Hippocampus Middle	brain

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