Variant report

Variant	rs2329717
Chromosome Location	chr21:45652644-45652645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45648743..45651558-chr21:45652534..45654668,2	K562	blood:
2	chr21:45571301..45575033-chr21:45652281..45654701,3	MCF-7	breast:
3	chr21:45647000..45652679-chr21:45655526..45663684,10	MCF-7	breast:
4	chr21:45620311..45631567-chr21:45651002..45670824,52	MCF-7	breast:
5	chr21:45642545..45644733-chr21:45651214..45653220,2	K562	blood:
6	chr21:45637874..45640737-chr21:45652531..45655334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000232124	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2329716	0.82[EUR][1000 genomes]
rs4511811	0.81[EUR][1000 genomes]
rs4819387	0.80[EUR][1000 genomes]
rs8134498	0.85[EUR][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
rs2329717	ICOSLG	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45628600-45659600	Weak transcription	Right Atrium	heart
2	chr21:45632200-45659600	Weak transcription	Fetal Kidney	kidney
3	chr21:45639800-45659400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:45640000-45659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr21:45640600-45653400	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr21:45641600-45654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr21:45643400-45653600	Weak transcription	HepG2	liver
8	chr21:45643400-45659600	Weak transcription	Hela-S3	cervix
9	chr21:45643600-45653400	Weak transcription	Left Ventricle	heart
10	chr21:45643600-45653400	Weak transcription	HMEC	breast
11	chr21:45643600-45653800	Weak transcription	Stomach Mucosa	stomach
12	chr21:45643600-45654400	Weak transcription	NHEK	skin
13	chr21:45643600-45654800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr21:45644800-45659400	Weak transcription	Small Intestine	intestine
15	chr21:45645200-45659200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr21:45645400-45653200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr21:45645800-45656600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr21:45646000-45653400	Weak transcription	Thymus	Thymus
19	chr21:45646000-45659000	Strong transcription	Fetal Intestine Small	intestine
20	chr21:45646200-45656400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:45646200-45657400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr21:45646200-45657400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:45646200-45658600	Strong transcription	Liver	Liver
24	chr21:45646200-45658800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr21:45646400-45657600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr21:45646800-45657000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr21:45646800-45658400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr21:45646800-45658800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr21:45647000-45652800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr21:45647000-45653200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr21:45647400-45657400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr21:45647800-45657400	Strong transcription	Colonic Mucosa	Colon
33	chr21:45647800-45657600	Strong transcription	Primary B cells from cord blood	blood
34	chr21:45648400-45656000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr21:45648400-45658400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr21:45649000-45653000	Weak transcription	HSMMtube	muscle
37	chr21:45649000-45655800	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr21:45649000-45658600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr21:45649200-45653000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr21:45650000-45653000	Weak transcription	Primary T cells from cord blood	blood
41	chr21:45650000-45653400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr21:45650200-45653000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr21:45650200-45653200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr21:45650400-45653000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr21:45650600-45652800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr21:45650600-45652800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr21:45650600-45653000	Weak transcription	Brain Anterior Caudate	brain
48	chr21:45650600-45653000	Weak transcription	Right Ventricle	heart
49	chr21:45650600-45653400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr21:45650600-45653400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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