Variant report

Variant	rs4319339
Chromosome Location	chr1:221916814-221916815
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	ATF2	chr1:221914976-221917478	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:221916617-221916919	HUVEC	blood vessel:	n/a	n/a
3	MAX	chr1:221914927-221916836	MCF-7	breast:	n/a	chr1:221916101-221916110 chr1:221916100-221916110
4	RAD21	chr1:221913441-221917304	IMR90	lung:	n/a	chr1:221916643-221916657 chr1:221915692-221915706
5	YY1	chr1:221915923-221916897	GM12878	blood:	n/a	chr1:221916268-221916282 chr1:221916491-221916502 chr1:221916830-221916839
6	CTBP2	chr1:221914861-221916839	H1-hESC	embryonic stem cell:	n/a	n/a
7	UBTF	chr1:221915704-221916886	K562	blood:	n/a	n/a
8	POLR2A	chr1:221915038-221916863	GM12878	blood:	n/a	n/a
9	CHD2	chr1:221914975-221917455	GM12878	blood:	n/a	chr1:221916212-221916222
10	POLR2A	chr1:221913461-221917502	GM18526	blood:	n/a	n/a
11	POLR2A	chr1:221914999-221916963	Hela-S3	cervix:	n/a	n/a
12	ZNF143	chr1:221915207-221916891	H1-hESC	embryonic stem cell:	n/a	chr1:221916190-221916208 chr1:221916381-221916399
13	POLR2A	chr1:221913364-221917603	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:221916593-221916934	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD1	chr1:221914149-221917620	GM12878	blood:	n/a	chr1:221916212-221916222
16	RFX5	chr1:221913575-221917269	SK-N-SH	brain:	n/a	chr1:221915670-221915679 chr1:221917085-221917094
17	BCLAF1	chr1:221915602-221917461	GM12878	blood:	n/a	chr1:221916273-221916286 chr1:221916645-221916658 chr1:221915692-221915705
18	RAD21	chr1:221914629-221916956	SK-N-SH_RA	brain:	n/a	chr1:221916643-221916657 chr1:221915692-221915706
19	POLR2A	chr1:221909168-221918546	GM12878	blood:	n/a	n/a
20	FOXM1	chr1:221916549-221917578	GM12878	blood:	n/a	n/a
21	RAD21	chr1:221915923-221916990	MCF-7	breast:	n/a	chr1:221916643-221916657
22	MAX	chr1:221915067-221917253	Hela-S3	cervix:	n/a	chr1:221916895-221916904 chr1:221916101-221916110 chr1:221916100-221916110
23	PAX5	chr1:221915936-221916854	GM12892	blood:	n/a	chr1:221916761-221916780 chr1:221916356-221916375
24	POLR2A	chr1:221915281-221916880	MCF-7	breast:	n/a	n/a
25	POLR2A	chr1:221915610-221917433	GM12891	blood:	n/a	n/a
26	POLR2A	chr1:221914975-221916939	K562	blood:	n/a	n/a
27	E2F4	chr1:221914753-221916884	K562	blood:	n/a	chr1:221916537-221916544 chr1:221915669-221915678 chr1:221916273-221916282 chr1:221915655-221915664 chr1:221914972-221914981 chr1:221916537-221916544 chr1:221916537-221916544 chr1:221916784-221916794 chr1:221916830-221916839 chr1:221916213-221916225
28	TBP	chr1:221914799-221916941	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr1:221916700-221916850	NHEK	skin:	n/a	n/a
30	RAD21	chr1:221914803-221917358	Hela-S3	cervix:	n/a	chr1:221916643-221916657 chr1:221915692-221915706
31	POLR2A	chr1:221915018-221917012	U87	brain:	n/a	n/a
32	POLR2A	chr1:221915063-221917414	GM12878	blood:	n/a	n/a
33	HDAC2	chr1:221916577-221916880	HepG2	liver:	n/a	n/a
34	RCOR1	chr1:221916217-221917458	GM12878	blood:	n/a	n/a
35	JUND	chr1:221914795-221917008	K562	blood:	n/a	chr1:221915656-221915665 chr1:221916765-221916774 chr1:221916021-221916035 chr1:221916217-221916226 chr1:221915505-221915514 chr1:221916221-221916230 chr1:221914973-221914982
36	ZBTB7A	chr1:221916196-221916877	K562	blood:	n/a	chr1:221916845-221916852
37	POLR2A	chr1:221916689-221916814	A549	lung:	n/a	n/a
38	POLR2A	chr1:221914985-221917487	GM12892	blood:	n/a	n/a
39	TCF7L2	chr1:221915048-221916863	HCT-116	colon:	n/a	n/a
40	POLR2A	chr1:221915227-221916875	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr1:221915043-221917379	GM10847	blood:	n/a	n/a
42	SMC3	chr1:221914702-221917371	Hela-S3	cervix:	n/a	chr1:221916489-221916499
43	RUNX3	chr1:221914699-221917421	GM12878	blood:	n/a	n/a
44	E2F6	chr1:221915527-221916839	A549	lung:	n/a	chr1:221916537-221916544 chr1:221915669-221915678 chr1:221916273-221916282 chr1:221915655-221915664 chr1:221916537-221916544 chr1:221916537-221916544 chr1:221916784-221916794 chr1:221916830-221916839 chr1:221916213-221916225
45	MYC	chr1:221914100-221916901	NB4	blood:	n/a	chr1:221916101-221916110 chr1:221916100-221916110
46	E2F6	chr1:221915840-221916881	H1-hESC	embryonic stem cell:	n/a	chr1:221916537-221916544 chr1:221916273-221916282 chr1:221916537-221916544 chr1:221916537-221916544 chr1:221916784-221916794 chr1:221916830-221916839 chr1:221916213-221916225
47	POLR2A	chr1:221914864-221916921	K562	blood:	n/a	n/a
48	POLR2A	chr1:221909243-221918347	GM12878	blood:	n/a	n/a
49	MAX	chr1:221915530-221916892	H1-hESC	embryonic stem cell:	n/a	chr1:221916101-221916110 chr1:221916100-221916110
50	POLR2A	chr1:221913221-221917867	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:221916288..221917841-chr1:221930894..221932532,2	MCF-7	breast:
2	chr1:221882652..221891989-chr1:221912814..221917285,15	K562	blood:
3	chr1:221651194..221651783-chr1:221916549..221917370,2	MCF-7	breast:
4	chr1:221910710..221913145-chr1:221916027..221918858,3	MCF-7	breast:
5	chr1:221915773..221917564-chr1:221920253..221922492,3	MCF-7	breast:
6	chr1:221916305..221918049-chr1:221927008..221929788,2	K562	blood:
7	chr1:221886657..221890286-chr1:221915663..221918002,3	MCF-7	breast:
8	chr1:221915847..221918268-chr1:222049176..222051061,2	K562	blood:
9	chr1:221914898..221917139-chr1:222150225..222152993,2	MCF-7	breast:
10	chr1:221915958..221917862-chr1:221982281..221984311,2	MCF-7	breast:
11	chr1:221915785..221917176-chr1:222059774..222060678,4	MCF-7	breast:
12	chr1:221915716..221917980-chr1:222052338..222055276,2	MCF-7	breast:
13	chr1:221915763..221917609-chr1:221970690..221972444,2	MCF-7	breast:

Variant related genes	Relation type
DUSP10	TF binding region
ENSG00000143507	Chromatin interaction
ENSG00000238042	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11118845	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1141714	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4317817	0.95[ASN][1000 genomes]
rs4846351	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6690778	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv3423401	chr1:221915354-221917902	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221911600-221917200	Active TSS	Brain Angular Gyrus	brain
2	chr1:221912800-221917000	Active TSS	Brain Hippocampus Middle	brain
3	chr1:221912800-221917000	Active TSS	Brain Substantia Nigra	brain
4	chr1:221912800-221917200	Active TSS	HSMMtube	muscle
5	chr1:221913000-221917400	Active TSS	Brain Cingulate Gyrus	brain
6	chr1:221913200-221917000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:221913200-221917000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:221913200-221917000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:221913200-221917000	Active TSS	NHLF	lung
10	chr1:221913200-221917400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:221913400-221917000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:221913400-221917000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:221913400-221917000	Active TSS	NHDF-Ad	bronchial
14	chr1:221913400-221917400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:221913600-221917000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:221913600-221917000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:221913600-221917000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr1:221913600-221917000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
19	chr1:221913600-221917200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:221913600-221917200	Active TSS	Right Atrium	heart
21	chr1:221913800-221917000	Active TSS	GM12878-XiMat	blood
22	chr1:221914000-221917000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:221914000-221917000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr1:221914000-221917000	Active TSS	Ovary	ovary
25	chr1:221914000-221917000	Active TSS	Placenta Amnion	Placenta Amnion
26	chr1:221914000-221917200	Active TSS	Psoas Muscle	Psoas
27	chr1:221914200-221917000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:221914200-221917000	Active TSS	Lung	lung
29	chr1:221914200-221917000	Active TSS	Pancreas	Pancrea
30	chr1:221914200-221917200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:221914200-221917200	Active TSS	Left Ventricle	heart
32	chr1:221914200-221917400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:221914400-221917000	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:221914400-221917000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:221914400-221917000	Active TSS	Aorta	Aorta
36	chr1:221914400-221917000	Active TSS	Esophagus	oesophagus
37	chr1:221914400-221917000	Active TSS	Stomach Mucosa	stomach
38	chr1:221914400-221917000	Active TSS	A549	lung
39	chr1:221914400-221917200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:221914400-221917400	Active TSS	Osteobl	bone
41	chr1:221914600-221917000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:221914600-221917000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:221914600-221917000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:221914600-221917000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:221914600-221917000	Active TSS	Fetal Kidney	kidney
46	chr1:221914600-221917200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr1:221914600-221917200	Active TSS	Right Ventricle	heart
48	chr1:221914800-221917000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:221914800-221917000	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:221914800-221917000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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