Variant report

Variant	rs10419883
Chromosome Location	chr19:45629269-45629270
allele	C/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	RAD21	chr19:45629250-45629663	HepG2	liver:	n/a	chr19:45629475-45629494
2	RAD21	chr19:45629099-45629810	MCF-7	breast:	n/a	chr19:45629475-45629494
3	SMC3	chr19:45629268-45629762	GM12878	blood:	n/a	chr19:45629479-45629493
4	MAX	chr19:45629244-45629723	K562	blood:	n/a	n/a
5	RAD21	chr19:45629263-45629680	ECC-1	luminal epithelium:	n/a	chr19:45629475-45629494
6	RAD21	chr19:45629194-45629724	HepG2	liver:	n/a	chr19:45629475-45629494
7	RAD21	chr19:45629198-45629685	A549	lung:	n/a	chr19:45629475-45629494
8	CTCF	chr19:45629213-45629743	MCF-7	breast:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
9	CTCF	chr19:45629238-45629690	HepG2	liver:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
10	SMC3	chr19:45629233-45629890	SK-N-SH	brain:	n/a	chr19:45629479-45629493
11	CTCF	chr19:45629220-45629370	HFF-Myc	foreskin:	n/a	n/a
12	RAD21	chr19:45629111-45629748	MCF-7	breast:	n/a	chr19:45629475-45629494
13	RUNX3	chr19:45629269-45629715	GM12878	blood:	n/a	n/a
14	PAX5	chr19:45629229-45629716	GM12892	blood:	n/a	n/a
15	PAX5	chr19:45629132-45629719	GM12878	blood:	n/a	n/a
16	RAD21	chr19:45629217-45629651	A549	lung:	n/a	chr19:45629475-45629494
17	MAX	chr19:45629107-45629721	A549	lung:	n/a	n/a
18	CTCF	chr19:45629228-45629785	MCF-7	breast:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
19	PAX5	chr19:45629224-45629674	GM12878	blood:	n/a	n/a
20	CTCF	chr19:45628986-45630203	A549	lung:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
21	MAX	chr19:45629181-45629784	MCF-7	breast:	n/a	n/a
22	RAD21	chr19:45629177-45629736	H1-hESC	embryonic stem cell:	n/a	chr19:45629475-45629494
23	CTCF	chr19:45628805-45629901	SK-N-SH	brain:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
24	MTA3	chr19:45629249-45629737	GM12878	blood:	n/a	n/a
25	MAX	chr19:45629204-45629747	ECC-1	luminal epithelium:	n/a	n/a
26	FOXM1	chr19:45629231-45629678	GM12878	blood:	n/a	n/a
27	RAD21	chr19:45629206-45629812	HCT-116	colon:	n/a	chr19:45629475-45629494
28	MAX	chr19:45629261-45629657	NB4	blood:	n/a	n/a
29	CTCF	chr19:45629245-45629689	H1-hESC	embryonic stem cell:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
30	RAD21	chr19:45629266-45629739	ECC-1	luminal epithelium:	n/a	chr19:45629475-45629494
31	GABPA	chr19:45629180-45629660	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr19:45629258-45629657	A549	lung:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
33	PAX5	chr19:45629174-45629662	GM12878	blood:	n/a	n/a
34	RAD21	chr19:45629263-45629651	SK-N-SH_RA	brain:	n/a	chr19:45629475-45629494
35	RAD21	chr19:45629260-45629734	H1-hESC	embryonic stem cell:	n/a	chr19:45629475-45629494
36	CTCF	chr19:45629215-45629835	HCT-116	colon:	n/a	chr19:45629478-45629494 chr19:45629472-45629493 chr19:45629479-45629492 chr19:45629477-45629495
37	RAD21	chr19:45629144-45629730	SK-N-SH	brain:	n/a	chr19:45629475-45629494

No.	Distal block	Cell Line	Cell type
1	chr19:45520309..45520814-chr19:45629032..45629876,2	K562	blood:
2	chr19:45519171..45521902-chr19:45628878..45631684,2	K562	blood:
3	chr19:45576178..45580996-chr19:45624559..45629632,6	MCF-7	breast:
4	chr19:45628639..45633572-chr19:45633990..45640719,7	K562	blood:
5	chr19:45573399..45575216-chr19:45628226..45630938,2	K562	blood:
6	chr19:45562534..45563370-chr19:45629042..45629617,2	MCF-7	breast:
7	chr19:45615379..45616248-chr19:45629125..45629890,2	MCF-7	breast:
8	chr19:45629050..45629922-chr19:45690474..45691467,2	K562	blood:
9	chr19:45580445..45584108-chr19:45627620..45631458,4	MCF-7	breast:
10	chr19:45628535..45631533-chr19:45631563..45633222,2	K562	blood:
11	chr19:45628826..45631533-chr19:45682194..45684783,2	MCF-7	breast:
12	chr19:45625755..45627868-chr19:45628373..45630846,2	K562	blood:
13	chr19:45626416..45630262-chr19:45631915..45636617,6	MCF-7	breast:
14	chr19:45627945..45630331-chr19:45681487..45684370,2	K562	blood:
15	chr19:45432095..45434023-chr19:45626902..45629320,2	K562	blood:
16	chr19:45593118..45596201-chr19:45627236..45629930,3	K562	blood:
17	chr19:45628901..45631522-chr19:45638053..45641235,4	K562	blood:
18	chr19:45628279..45631709-chr19:45631914..45634040,3	MCF-7	breast:
19	chr19:45593118..45596543-chr19:45627236..45631032,6	K562	blood:
20	chr19:45582126..45584327-chr19:45628137..45630389,2	MCF-7	breast:

Variant related genes	Relation type
EIF5AP3	TF binding region
ENSG00000007047	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000267348	Chromatin interaction
ENSG00000007255	Chromatin interaction
ENSG00000170684	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000267044	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000267346	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000266958	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10402479	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405306	0.81[AFR][1000 genomes]
rs10405721	0.81[AFR][1000 genomes]
rs10406911	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408366	0.81[AFR][1000 genomes]
rs10408462	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409232	0.84[AFR][1000 genomes]
rs10409903	0.81[AFR][1000 genomes]
rs10410424	0.80[YRI][hapmap]
rs10415674	0.80[YRI][hapmap];0.92[AFR][1000 genomes]
rs10417347	0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417618	0.81[AFR][1000 genomes]
rs10419874	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420824	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421085	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422671	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423555	0.80[YRI][hapmap];0.92[AFR][1000 genomes]
rs10425380	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1076384	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12459386	1.00[AMR][1000 genomes]
rs12461749	1.00[AMR][1000 genomes]
rs13344055	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13344075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16979688	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2003183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2003345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2004356	0.88[AFR][1000 genomes]
rs2041261	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2043320	0.88[AFR][1000 genomes]
rs2060252	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2060253	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28404390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28657408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28706378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35904300	1.00[AMR][1000 genomes]
rs4803798	0.81[AFR][1000 genomes]
rs56764148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58600209	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60455813	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7257599	0.80[YRI][hapmap]
rs733289	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs73562286	1.00[AMR][1000 genomes]
rs747646	0.88[AFR][1000 genomes]
rs747647	0.88[AFR][1000 genomes]
rs754364	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs754367	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs892133	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45606800-45634000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr19:45608000-45639400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr19:45610400-45644400	Weak transcription	Aorta	Aorta
4	chr19:45615600-45629800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:45617000-45651600	Weak transcription	Fetal Kidney	kidney
6	chr19:45617400-45633200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:45617800-45640000	Weak transcription	Fetal Lung	lung
8	chr19:45618800-45639600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:45618800-45639600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:45620000-45633400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:45620800-45643800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:45621000-45629400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:45621000-45634000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr19:45621000-45634000	Weak transcription	HSMMtube	muscle
15	chr19:45621200-45629600	Weak transcription	HepG2	liver
16	chr19:45621200-45633800	Weak transcription	Osteobl	bone
17	chr19:45621200-45639800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:45621200-45644000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr19:45621400-45633400	Weak transcription	Dnd41	blood
20	chr19:45621400-45635000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:45621600-45643800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:45621800-45639800	Weak transcription	Colon Smooth Muscle	Colon
23	chr19:45622000-45639200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:45622200-45633600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:45622200-45639600	Weak transcription	Fetal Brain Female	brain
26	chr19:45623000-45633600	Weak transcription	HSMM	muscle
27	chr19:45624400-45629600	Enhancers	Placenta	Placenta
28	chr19:45625000-45654200	Weak transcription	NHDF-Ad	bronchial
29	chr19:45625600-45637000	Weak transcription	Primary B cells from cord blood	blood
30	chr19:45625800-45636800	Weak transcription	Primary T cells from cord blood	blood
31	chr19:45626200-45644400	Weak transcription	Ovary	ovary
32	chr19:45626200-45653400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr19:45627000-45639200	Weak transcription	Brain Germinal Matrix	brain
34	chr19:45627200-45640000	Weak transcription	Adipose Nuclei	Adipose
35	chr19:45627400-45633200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr19:45627400-45633400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:45627400-45633400	Weak transcription	NHLF	lung
38	chr19:45627400-45633600	Weak transcription	HMEC	breast
39	chr19:45627600-45629400	Weak transcription	Fetal Brain Male	brain
40	chr19:45627600-45633800	Weak transcription	NHEK	skin
41	chr19:45627600-45655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:45627800-45629800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr19:45627800-45644000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr19:45628000-45632000	Weak transcription	Lung	lung
45	chr19:45628000-45633400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:45628000-45634000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:45628000-45634200	Weak transcription	Esophagus	oesophagus
48	chr19:45628200-45629400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:45628800-45629400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr19:45628800-45629400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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