Variant report

Variant	rs2838508
Chromosome Location	chr21:45586002-45586003
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	chr21:45585072..45590786-chr21:45590904..45593996,5	K562	blood:
2	chr21:45584708..45587339-chr21:45625931..45628312,2	MCF-7	breast:
3	chr21:45585070..45587795-chr21:45647222..45649775,2	K562	blood:
4	chr21:45582972..45588290-chr21:45588610..45593083,12	MCF-7	breast:
5	chr21:45585105..45587021-chr21:45670091..45672231,2	MCF-7	breast:
6	chr21:45584635..45586624-chr21:45659236..45661002,2	MCF-7	breast:
7	chr21:45585260..45589365-chr21:45591122..45593213,3	K562	blood:
8	chr21:45579145..45582773-chr21:45583367..45588421,9	K562	blood:
9	chr21:45564255..45569334-chr21:45585754..45591354,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000160223	Chromatin interaction
ENSG00000142182	Chromatin interaction
ENSG00000267913	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000225331	Chromatin interaction
ENSG00000232010	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1005046	0.89[CEU][hapmap]
rs1051981	0.93[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.88[TSI][hapmap]
rs11089117	0.88[EUR][1000 genomes]
rs11702859	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13048791	0.84[JPT][hapmap]
rs13049059	0.82[TSI][hapmap]
rs17004630	0.81[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap]
rs2006694	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2020945	0.90[TSI][hapmap]
rs2071135	0.80[CEU][hapmap]
rs2071142	0.91[TSI][hapmap]
rs2071143	0.87[TSI][hapmap]
rs2071154	0.92[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs2187313	0.81[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs2243999	0.91[TSI][hapmap]
rs2251267	0.87[TSI][hapmap]
rs2255828	0.88[TSI][hapmap]
rs2255955	0.85[JPT][hapmap]
rs2276532	0.92[JPT][hapmap]
rs2277805	0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs2277806	0.84[TSI][hapmap]
rs2299816	0.85[JPT][hapmap]
rs2299817	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2838464	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2838469	0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs2838486	0.88[TSI][hapmap]
rs2838490	0.91[TSI][hapmap]
rs2838491	0.87[TSI][hapmap]
rs2838502	0.91[TSI][hapmap]
rs2838503	0.88[TSI][hapmap]
rs2838507	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2838509	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	0.83[CEU][hapmap];0.86[EUR][1000 genomes]
rs34137354	0.98[ASN][1000 genomes]
rs34486701	0.88[ASN][1000 genomes]
rs3788104	0.81[CHB][hapmap]
rs3788108	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4818886	0.81[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs4819361	0.85[JPT][hapmap]
rs4819375	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs4819376	0.91[TSI][hapmap]
rs57683928	0.98[ASN][1000 genomes]
rs7277269	0.87[TSI][hapmap]
rs7280558	0.88[TSI][hapmap]
rs7282324	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs756554	0.87[TSI][hapmap]
rs7676	0.81[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.88[TSI][hapmap]
rs885872	0.81[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs915774	0.82[TSI][hapmap]
rs9306172	0.87[TSI][hapmap]
rs965733	0.96[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs968713	0.83[JPT][hapmap]
rs968714	0.87[TSI][hapmap]
rs9985064	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2838508	PWP2	cis	parietal	SCAN
rs2838508	TRAPPC10	cis	cerebellum	SCAN
rs2838508	KRTAP12-1	cis	cerebellum	SCAN
rs2838508	C21orf33	cis	parietal	SCAN
rs2838508	PWP2	cis	Muscle Skeletal	GTEx
rs2838508	PWP2	Cis_1M	lymphoblastoid	RTeQTL
rs2838508	C21orf129	cis	cerebellum	SCAN
rs2838508	ABCG1	cis	cerebellum	SCAN

Chromatin state (count:70 , 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	chr21:45580800-45586600	Weak transcription	Right Ventricle	heart
6	chr21:45580800-45589200	Weak transcription	Colonic Mucosa	Colon
7	chr21:45581000-45586200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr21:45581000-45586400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr21:45581000-45590400	Weak transcription	Pancreas	Pancrea
10	chr21:45581000-45591600	Weak transcription	Right Atrium	heart
11	chr21:45581200-45586600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr21:45581200-45589000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr21:45581400-45586400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr21:45581400-45586800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr21:45581600-45586200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr21:45582000-45586400	Weak transcription	Adipose Nuclei	Adipose
17	chr21:45582000-45587400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr21:45582400-45586800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr21:45583200-45587400	Enhancers	Stomach Mucosa	stomach
20	chr21:45584000-45586600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr21:45584200-45598800	Weak transcription	Ovary	ovary
22	chr21:45584400-45586800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:45584400-45587000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr21:45584400-45587800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr21:45584600-45586200	Weak transcription	Spleen	Spleen
26	chr21:45584600-45586800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr21:45584600-45587000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr21:45584600-45587200	Enhancers	Primary B cells from peripheral blood	blood
29	chr21:45584600-45587200	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr21:45584600-45587400	Enhancers	Brain Substantia Nigra	brain
31	chr21:45584600-45588000	Enhancers	Primary hematopoietic stem cells	blood
32	chr21:45584600-45588000	Enhancers	Fetal Thymus	thymus
33	chr21:45584600-45590200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr21:45584800-45586400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr21:45584800-45586400	Enhancers	Fetal Muscle Trunk	muscle
36	chr21:45584800-45586800	Enhancers	Esophagus	oesophagus
37	chr21:45584800-45586800	Enhancers	Gastric	stomach
38	chr21:45584800-45586800	Enhancers	HMEC	breast
39	chr21:45584800-45587200	Enhancers	Brain Anterior Caudate	brain
40	chr21:45584800-45587200	Enhancers	Brain Cingulate Gyrus	brain
41	chr21:45584800-45587200	Enhancers	Brain Hippocampus Middle	brain
42	chr21:45584800-45587600	Enhancers	Fetal Muscle Leg	muscle
43	chr21:45584800-45587600	Enhancers	Lung	lung
44	chr21:45584800-45588400	Enhancers	Primary B cells from cord blood	blood
45	chr21:45584800-45589200	Weak transcription	Fetal Intestine Small	intestine
46	chr21:45585000-45586400	Enhancers	Duodenum Mucosa	Duodenum
47	chr21:45585000-45586600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr21:45585000-45587000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr21:45585000-45587600	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr21:45585200-45586400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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