Variant report

Variant	rs9978109
Chromosome Location	chr21:45547913-45547914
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45546961..45549200-chr21:45595303..45598230,2	K562	blood:
2	chr21:45525708..45535025-chr21:45544493..45558414,30	MCF-7	breast:
3	chr21:45547494..45550018-chr21:45659282..45662155,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237604	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000241945	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1005045	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11910604	0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs2020943	1.00[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2071144	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227265	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838463	1.00[TSI][hapmap]
rs2838465	1.00[JPT][hapmap]
rs2838470	1.00[CEU][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2838479	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2838484	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2838487	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838495	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838497	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2838510	0.85[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap]
rs28834388	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57812760	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57855582	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60503863	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61689295	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62226718	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62226719	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62226722	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62226723	0.92[EUR][1000 genomes]
rs62226724	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275501	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7282644	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73909115	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8128926	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878132	1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9284512	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306175	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974767	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9975436	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9977122	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9978772	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9979931	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9980021	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980063	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9982695	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9982907	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9983551	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9983596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9978109	PWP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45528200-45552800	Weak transcription	Right Atrium	heart
2	chr21:45528600-45551800	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr21:45528800-45551800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr21:45528800-45551800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:45528800-45552000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr21:45528800-45552000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr21:45528800-45552000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr21:45528800-45552200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr21:45528800-45552200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr21:45528800-45552400	Weak transcription	Fetal Heart	heart
11	chr21:45528800-45552400	Strong transcription	Fetal Intestine Small	intestine
12	chr21:45528800-45552600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr21:45529000-45549200	Strong transcription	HepG2	liver
14	chr21:45529000-45549400	Strong transcription	HMEC	breast
15	chr21:45529000-45551000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr21:45529000-45551200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr21:45529000-45552000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr21:45529000-45552000	Strong transcription	Fetal Brain Female	brain
19	chr21:45529200-45551200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr21:45529200-45551200	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr21:45529200-45551400	Strong transcription	Ovary	ovary
22	chr21:45529200-45551800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr21:45529200-45551800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr21:45529200-45551800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr21:45529200-45552000	Strong transcription	Brain Germinal Matrix	brain
26	chr21:45529200-45552000	Strong transcription	Left Ventricle	heart
27	chr21:45529400-45551000	Strong transcription	Primary T cells from cord blood	blood
28	chr21:45529400-45551200	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr21:45529400-45551400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr21:45529400-45552200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr21:45529600-45552000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr21:45530000-45551400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr21:45530000-45552200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr21:45530200-45550800	Strong transcription	Dnd41	blood
35	chr21:45530600-45552600	Weak transcription	Fetal Brain Male	brain
36	chr21:45532000-45551200	Strong transcription	Pancreas	Pancrea
37	chr21:45532000-45551200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr21:45532400-45551400	Strong transcription	Colonic Mucosa	Colon
39	chr21:45532600-45551800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr21:45532600-45552800	Weak transcription	Fetal Kidney	kidney
41	chr21:45532800-45551600	Strong transcription	Stomach Smooth Muscle	stomach
42	chr21:45533200-45552400	Strong transcription	Fetal Stomach	stomach
43	chr21:45533400-45552200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr21:45533400-45552200	Strong transcription	NHLF	lung
45	chr21:45533600-45548800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr21:45533800-45551400	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr21:45533800-45551600	Strong transcription	Fetal Intestine Large	intestine
48	chr21:45534000-45550200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr21:45534000-45551000	Strong transcription	Rectal Smooth Muscle	rectum
50	chr21:45534000-45551400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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