Variant report

Variant	rs13051949
Chromosome Location	chr21:40760605-40760606
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr21:40760532-40760722	HepG2	liver:	n/a	n/a
2	ZNF263	chr21:40759838-40760901	HEK293-T-REx	kidney:	n/a	n/a
3	CTCF	chr21:40760600-40760750	NHEK	skin:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
4	CTCF	chr21:40760600-40760750	AG09319	gingival:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
5	RFX5	chr21:40760589-40760670	GM12878	blood:	n/a	n/a
6	POLR2A	chr21:40759490-40760859	GM12892	blood:	n/a	n/a
7	CTCF	chr21:40760600-40760750	HCPEpiC	choroid plexus:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
8	MAX	chr21:40759989-40760986	MCF-7	breast:	n/a	n/a
9	CTCF	chr21:40760524-40760817	MCF-7	breast:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
10	CHD1	chr21:40760531-40760757	H1-hESC	embryonic stem cell:	n/a	n/a
11	CEBPB	chr21:40760317-40760722	K562	blood:	n/a	n/a
12	POLR2A	chr21:40760124-40760727	GM12891	blood:	n/a	n/a
13	MAZ	chr21:40760425-40760824	Hela-S3	cervix:	n/a	n/a
14	CHD1	chr21:40760521-40760721	GM12878	blood:	n/a	n/a
15	CTCF	chr21:40760526-40760822	K562	blood:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
16	RAD21	chr21:40760413-40760860	SK-N-SH_RA	brain:	n/a	chr21:40760667-40760686 chr21:40760814-40760823
17	CTCF	chr21:40760528-40760837	ProgFib	skin:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
18	TBP	chr21:40760258-40760913	H1-hESC	embryonic stem cell:	n/a	n/a
19	RCOR1	chr21:40759400-40760859	K562	blood:	n/a	n/a
20	POLR2A	chr21:40759943-40760765	GM12891	blood:	n/a	n/a
21	GABPA	chr21:40760411-40760872	H1-hESC	embryonic stem cell:	n/a	chr21:40760800-40760814 chr21:40760625-40760639 chr21:40760803-40760812
22	FOXP2	chr21:40760466-40760852	SK-N-MC	brain:	n/a	n/a
23	ZEB1	chr21:40760556-40760792	GM12878	blood:	n/a	n/a
24	CTCF	chr21:40760600-40760750	GM12873	blood:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
25	CTCF	chr21:40760352-40760863	K562	blood:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
26	CTCF	chr21:40760560-40760710	WI-38	lung:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
27	CTCF	chr21:40760600-40760750	WI-38	lung:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
28	HCFC1	chr21:40759378-40760920	K562	blood:	n/a	n/a
29	TBP	chr21:40760507-40760715	HepG2	liver:	n/a	n/a
30	MAX	chr21:40760134-40760870	Hela-S3	cervix:	n/a	n/a
31	TAF7	chr21:40760330-40760846	H1-hESC	embryonic stem cell:	n/a	n/a
32	PAX5	chr21:40760447-40760870	GM12892	blood:	n/a	chr21:40760626-40760635
33	CTCF	chr21:40760600-40760750	HCT-116	colon:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
34	POLR2A	chr21:40760059-40760812	GM12891	blood:	n/a	n/a
35	CTCF	chr21:40760539-40760824	Lung_OC	lung:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
36	ZBTB7A	chr21:40760582-40760861	K562	blood:	n/a	n/a
37	EGR1	chr21:40760507-40760918	K562	blood:	n/a	chr21:40760626-40760635
38	POLR2A	chr21:40760405-40760790	MCF-7	breast:	n/a	n/a
39	CTCF	chr21:40760541-40760822	Medullo	brain:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
40	MXI1	chr21:40760421-40760871	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr21:40760473-40760799	K562	blood:	n/a	chr21:40760667-40760686
42	CTCF	chr21:40760600-40760750	HMF	breast:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
43	YY1	chr21:40760224-40760865	GM12878	blood:	n/a	chr21:40760800-40760814 chr21:40760798-40760809 chr21:40760791-40760805
44	POLR2A	chr21:40760460-40760743	GM12878	blood:	n/a	n/a
45	ZNF143	chr21:40760397-40760856	H1-hESC	embryonic stem cell:	n/a	chr21:40760795-40760805
46	RAD21	chr21:40760446-40760849	HepG2	liver:	n/a	chr21:40760667-40760686 chr21:40760814-40760823
47	CTCF	chr21:40760600-40760750	HL-60	blood:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686
48	TAF1	chr21:40760308-40760727	GM12891	blood:	n/a	n/a
49	MAX	chr21:40759361-40761054	MCF-7	breast:	n/a	chr21:40759619-40759629 chr21:40759797-40759807
50	CTCF	chr21:40760579-40760795	HUVEC	blood vessel:	n/a	chr21:40760669-40760687 chr21:40760671-40760684 chr21:40760671-40760684 chr21:40760664-40760685 chr21:40760670-40760686

No.	Distal block	Cell Line	Cell type
1	chr21:40685384..40686352-chr21:40760120..40761140,5	MCF-7	breast:
2	chr21:40684466..40689800-chr21:40758261..40763098,10	K562	blood:
3	chr21:40759594..40762847-chr21:40823318..40826677,3	K562	blood:
4	chr21:40745293..40746195-chr21:40759850..40760932,7	MCF-7	breast:
5	chr21:40757591..40761225-chr21:40763023..40767191,7	K562	blood:
6	chr21:40708669..40709220-chr21:40760212..40761168,2	K562	blood:
7	chr21:40693463..40696053-chr21:40759629..40761307,2	MCF-7	breast:
8	chr21:40758499..40762376-chr21:40796781..40799288,3	K562	blood:
9	chr21:40759156..40760884-chr21:40816362..40818324,3	K562	blood:
10	chr21:40746451..40749340-chr21:40759411..40761167,2	MCF-7	breast:
11	chr21:40671488..40672356-chr21:40760178..40761118,2	MCF-7	breast:
12	chr21:40684332..40690368-chr21:40756970..40764337,16	K562	blood:
13	chr21:40750855..40754449-chr21:40757264..40761324,13	K562	blood:
14	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
15	chr21:40759725..40763162-chr21:40764409..40767950,4	K562	blood:
16	chr21:40552516..40555515-chr21:40758943..40760790,2	MCF-7	breast:
17	chr21:40750751..40754678-chr21:40755594..40761324,12	K562	blood:
18	chr21:40760590..40763335-chr21:40800736..40802529,2	K562	blood:
19	chr21:40717665..40724454-chr21:40756191..40763334,22	MCF-7	breast:
20	chr21:40685529..40686310-chr21:40760206..40761070,2	K562	blood:
21	chr21:40552621..40555799-chr21:40758034..40760615,3	K562	blood:
22	chr21:40748679..40750814-chr21:40758912..40761248,3	K562	blood:
23	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
24	chr21:40755802..40758273-chr21:40758369..40760779,2	MCF-7	breast:
25	chr21:40759594..40762847-chr21:40822621..40825193,3	K562	blood:
26	chr21:40716079..40725440-chr21:40756737..40764615,26	K562	blood:
27	21:40687235-40690033..21:40757151-40764378	K562	blood:
28	chr21:40760349..40761906-chr21:40811512..40813865,2	K562	blood:
29	chr21:40750392..40754801-chr21:40757428..40762186,12	MCF-7	breast:
30	chr21:40748679..40750675-chr21:40758576..40761248,3	K562	blood:
31	chr21:40550674..40556725-chr21:40756529..40762932,9	MCF-7	breast:
32	chr21:40717517..40723762-chr21:40756232..40761980,18	MCF-7	breast:
33	21:40686083-40686932..21:40757151-40764378	K562	blood:
34	chr21:40760487..40761081-chr21:40813246..40814131,2	MCF-7	breast:
35	chr21:40758008..40760801-chr21:40816074..40819285,3	MCF-7	breast:
36	chr21:40758092..40760884-chr21:40816362..40818206,3	K562	blood:
37	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
38	chr21:40716442..40724032-chr21:40756185..40762223,18	K562	blood:
39	chr21:40760208..40762465-chr21:40802596..40804503,2	K562	blood:
40	chr21:40750891..40755008-chr21:40755976..40761346,13	MCF-7	breast:
41	chr21:40751647..40752183-chr21:40760227..40760802,2	K562	blood:
42	chr21:40759292..40761069-chr21:40781933..40784921,2	MCF-7	breast:
43	chr21:40685180..40686016-chr21:40760150..40760802,2	MCF-7	breast:

Variant related genes	Relation type
WRB	TF binding region
ENSG00000238556	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000252915	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000185658	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000205581	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1060180	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775662	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701047	0.82[EUR][1000 genomes]
rs13051571	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13230	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094874	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2244352	0.81[ASN][1000 genomes]
rs2299739	0.83[EUR][1000 genomes]
rs2299741	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836994	0.81[ASN][1000 genomes]
rs2836997	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2836998	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836999	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837000	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837001	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837002	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837003	0.83[ASN][1000 genomes]
rs2837004	0.83[ASN][1000 genomes]
rs2837005	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837006	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837007	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837008	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787923	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3787924	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4816624	0.88[ASN][1000 genomes]
rs4818035	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818036	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6517547	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131718	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305674	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974828	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1056452	chr21:40741893-40782587	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1063521	chr21:40747754-40790197	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs13051949	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs13051949	LCA5L	cis	Artery Tibial	GTEx
rs13051949	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs13051949	WRB	cis	Artery Aorta	GTEx
rs13051949	LCA5L	cis	Esophagus Mucosa	GTEx
rs13051949	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs13051949	LCA5L	cis	Heart Left Ventricle	GTEx
rs13051949	WRB	cis	Nerve Tibial	GTEx
rs13051949	LCA5L	cis	Whole Blood	GTEx
rs13051949	LCA5L	cis	Esophagus Muscularis	GTEx
rs13051949	LCA5L	cis	Nerve Tibial	GTEx
rs13051949	WRB	cis	lung	GTEx
rs13051949	LCA5L	cis	Thyroid	GTEx
rs13051949	WRB	cis	Esophagus Mucosa	GTEx
rs13051949	WRB	cis	Artery Tibial	GTEx
rs13051949	LCA5L	cis	Artery Aorta	GTEx
rs13051949	WRB	cis	Thyroid	GTEx
rs13051949	LCA5L	cis	Stomach	GTEx
rs13051949	WRB	cis	Esophagus Muscularis	GTEx
rs13051949	WRB	cis	Adipose Subcutaneous	GTEx
rs13051949	WRB	cis	Whole Blood	GTEx
rs13051949	LCA5L	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40759200-40761000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr21:40759400-40760800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr21:40759400-40760800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr21:40759400-40760800	Active TSS	Colon Smooth Muscle	Colon
5	chr21:40759400-40761000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr21:40759400-40761000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr21:40759400-40761000	Active TSS	Psoas Muscle	Psoas
8	chr21:40759400-40761000	Active TSS	A549	lung
9	chr21:40759400-40761400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr21:40759600-40761000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:40759600-40761000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr21:40759800-40761000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:40759800-40761000	Flanking Active TSS	Fetal Brain Female	brain
14	chr21:40760000-40760800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr21:40760000-40760800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr21:40760000-40760800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr21:40760000-40760800	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr21:40760000-40760800	Flanking Active TSS	Placenta	Placenta
19	chr21:40760000-40760800	Flanking Active TSS	Fetal Stomach	stomach
20	chr21:40760000-40760800	Flanking Active TSS	Thymus	Thymus
21	chr21:40760000-40760800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr21:40760000-40761000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr21:40760000-40761000	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr21:40760000-40761000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr21:40760000-40761000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr21:40760000-40761000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr21:40760000-40761000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr21:40760000-40761000	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr21:40760000-40761000	Flanking Active TSS	Fetal Muscle Trunk	muscle
30	chr21:40760000-40761000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr21:40760000-40761000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr21:40760000-40761000	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr21:40760000-40761000	Flanking Active TSS	Hela-S3	cervix
34	chr21:40760000-40761000	Flanking Active TSS	HepG2	liver
35	chr21:40760000-40761000	Flanking Active TSS	NHEK	skin
36	chr21:40760000-40761200	Flanking Active TSS	Dnd41	blood
37	chr21:40760200-40760800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr21:40760200-40760800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr21:40760200-40760800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr21:40760200-40760800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr21:40760200-40760800	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr21:40760200-40760800	Flanking Active TSS	Colonic Mucosa	Colon
43	chr21:40760200-40760800	Flanking Active TSS	Fetal Intestine Large	intestine
44	chr21:40760200-40760800	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr21:40760200-40760800	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr21:40760200-40761000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr21:40760200-40761000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr21:40760200-40761000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr21:40760200-40761000	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr21:40760200-40761000	Flanking Active TSS	Ovary	ovary

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