Variant report

Variant	rs2838509
Chromosome Location	chr21:45587728-45587729
allele	C/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:12)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45586912..45588544-chr21:45664966..45667379,2	K562	blood:
2	chr21:45581288..45584070-chr21:45586807..45588482,3	MCF-7	breast:
3	chr21:45585072..45590786-chr21:45590904..45593996,5	K562	blood:
4	chr21:45585070..45587795-chr21:45647222..45649775,2	K562	blood:
5	chr21:45563215..45565745-chr21:45586840..45589212,2	K562	blood:
6	chr21:45571920..45573873-chr21:45586886..45589109,2	MCF-7	breast:
7	chr21:45582972..45588290-chr21:45588610..45593083,12	MCF-7	breast:
8	chr21:45586838..45589344-chr21:45614842..45616536,2	MCF-7	breast:
9	chr21:45567167..45569134-chr21:45587063..45589096,2	MCF-7	breast:
10	chr21:45585260..45589365-chr21:45591122..45593213,3	K562	blood:
11	chr21:45579145..45582773-chr21:45583367..45588421,9	K562	blood:
12	chr21:45564255..45569334-chr21:45585754..45591354,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ICOSLG-5	chr21:45587386-45588035	XLOC_014111

No data

Variant related genes	Relation type
ENSG00000225331	Chromatin interaction
ENSG00000267913	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1005046	0.84[CEU][hapmap]
rs1051981	0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[TSI][hapmap]
rs11089117	0.86[EUR][1000 genomes]
rs11702859	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13048791	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs17004630	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs2006694	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2020945	0.90[TSI][hapmap]
rs2071135	0.80[CEU][hapmap]
rs2071142	0.90[TSI][hapmap]
rs2071143	0.87[TSI][hapmap]
rs2071154	0.90[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs2187313	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap]
rs2243999	0.90[TSI][hapmap]
rs2251267	0.87[TSI][hapmap]
rs2255828	0.81[TSI][hapmap]
rs2255955	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2276532	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2277805	0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap]
rs2277806	0.84[TSI][hapmap]
rs2299816	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2299817	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2838464	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2838469	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs2838486	0.81[TSI][hapmap]
rs2838490	0.90[TSI][hapmap]
rs2838491	0.87[TSI][hapmap]
rs2838502	0.90[TSI][hapmap]
rs2838503	0.87[TSI][hapmap]
rs2838507	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2838508	1.00[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838511	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs34137354	1.00[ASN][1000 genomes]
rs34486701	0.90[ASN][1000 genomes]
rs3788104	1.00[CHB][hapmap]
rs3788108	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4818886	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs4819361	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4819362	0.81[CHB][hapmap]
rs4819375	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4819376	0.90[TSI][hapmap]
rs57683928	1.00[ASN][1000 genomes]
rs7277269	0.87[TSI][hapmap]
rs7280558	0.87[TSI][hapmap]
rs7282324	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs756554	0.87[TSI][hapmap]
rs7676	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.87[TSI][hapmap]
rs885872	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap]
rs915774	0.82[TSI][hapmap]
rs9306172	0.87[TSI][hapmap]
rs965733	0.90[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs968713	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs968714	0.87[TSI][hapmap]
rs9985064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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	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
7	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
8	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
9	nsv913891	chr21:45508561-45588518	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv913892	chr21:45508561-45595060	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer 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
11	nsv913893	chr21:45508561-45603746	Flanking Active TSS Strong transcription Genic enhancers Active TSS 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
12	nsv913894	chr21:45508561-45627976	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv913895	chr21:45528919-45595060	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv913896	chr21:45528919-45603746	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv1065479	chr21:45571324-45617878	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv913899	chr21:45577102-45611950	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
23	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2838509	PWP2	cis	parietal	SCAN
rs2838509	C21orf33	cis	parietal	SCAN
rs2838509	KRTAP12-1	cis	cerebellum	SCAN
rs2838509	C21orf129	cis	cerebellum	SCAN
rs2838509	PWP2	Cis_1M	lymphoblastoid	RTeQTL
rs2838509	ABCG1	cis	cerebellum	SCAN
rs2838509	TRAPPC10	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45575400-45592000	Weak transcription	Fetal Brain Female	brain
2	chr21:45579800-45590400	Weak transcription	Colon Smooth Muscle	Colon
3	chr21:45579800-45590400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr21:45580000-45591200	Weak transcription	Fetal Heart	heart
5	chr21:45580800-45589200	Weak transcription	Colonic Mucosa	Colon
6	chr21:45581000-45590400	Weak transcription	Pancreas	Pancrea
7	chr21:45581000-45591600	Weak transcription	Right Atrium	heart
8	chr21:45581200-45589000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr21:45584200-45598800	Weak transcription	Ovary	ovary
10	chr21:45584400-45587800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr21:45584600-45588000	Enhancers	Primary hematopoietic stem cells	blood
12	chr21:45584600-45588000	Enhancers	Fetal Thymus	thymus
13	chr21:45584600-45590200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr21:45584800-45588400	Enhancers	Primary B cells from cord blood	blood
15	chr21:45584800-45589200	Weak transcription	Fetal Intestine Small	intestine
16	chr21:45585800-45587800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr21:45585800-45588000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr21:45585800-45588400	Enhancers	Primary T cells from cord blood	blood
19	chr21:45586000-45587800	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr21:45586000-45587800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr21:45586200-45587800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr21:45586400-45589600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr21:45586400-45592400	Weak transcription	HUVEC	blood vessel
24	chr21:45586600-45587800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr21:45586600-45587800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr21:45586600-45589400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr21:45586800-45588000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr21:45586800-45588000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr21:45586800-45589000	Weak transcription	Gastric	stomach
30	chr21:45586800-45589600	Weak transcription	Liver	Liver
31	chr21:45586800-45590400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr21:45586800-45592200	Weak transcription	Brain Angular Gyrus	brain
33	chr21:45587200-45590600	Weak transcription	Right Ventricle	heart
34	chr21:45587200-45591600	Weak transcription	Brain Anterior Caudate	brain
35	chr21:45587200-45591600	Weak transcription	Brain Hippocampus Middle	brain
36	chr21:45587200-45592200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr21:45587200-45592200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr21:45587400-45587800	Weak transcription	Brain Substantia Nigra	brain
39	chr21:45587400-45588000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr21:45587400-45589400	Weak transcription	Stomach Mucosa	stomach
41	chr21:45587400-45590000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr21:45587400-45592400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr21:45587600-45588000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr21:45587600-45588000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr21:45587600-45588400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr21:45587600-45588600	Enhancers	Primary B cells from peripheral blood	blood
47	chr21:45587600-45589600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr21:45587600-45589600	Weak transcription	Spleen	Spleen
49	chr21:45587600-45590000	Weak transcription	GM12878-XiMat	blood
50	chr21:45587600-45590200	Weak transcription	Lung	lung

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