Variant report

Variant	rs4344301
Chromosome Location	chr1:228784259-228784260
allele	G/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	chr1:228782936-228784291	MCF-7	breast:	n/a	chr1:228784239-228784249
2	BRCA1	chr1:228783354-228784332	Hela-S3	cervix:	n/a	chr1:228783960-228783967
3	SMARCB1	chr1:228782483-228784310	Hela-S3	cervix:	n/a	n/a
4	GATA3	chr1:228783064-228784303	A549	lung:	n/a	n/a
5	POLR2A	chr1:228782361-228784289	Hela-S3	cervix:	n/a	n/a
6	TCF7L2	chr1:228782917-228784324	Hela-S3	cervix:	n/a	n/a
7	CHD2	chr1:228782398-228784265	Hela-S3	cervix:	n/a	chr1:228783099-228783109 chr1:228783311-228783321 chr1:228783805-228783812
8	TBP	chr1:228782430-228785001	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:228782342-228784357	Hela-S3	cervix:	n/a	n/a
10	MAX	chr1:228782832-228784338	HepG2	liver:	n/a	chr1:228784239-228784249
11	MAX	chr1:228782411-228784428	A549	lung:	n/a	chr1:228784239-228784249
12	REST	chr1:228783171-228784271	A549	lung:	n/a	chr1:228783513-228783526
13	E2F6	chr1:228782746-228784281	H1-hESC	embryonic stem cell:	n/a	chr1:228783805-228783812 chr1:228783095-228783105 chr1:228783096-228783107 chr1:228783096-228783104 chr1:228783095-228783106 chr1:228783943-228783952 chr1:228783084-228783098 chr1:228783096-228783103 chr1:228783384-228783396 chr1:228783096-228783104
14	MAX	chr1:228782406-228784444	HCT-116	colon:	n/a	chr1:228784239-228784249
15	POLR2A	chr1:228782353-228785134	MCF10A-Er-Src	breast:	n/a	n/a
16	YY1	chr1:228783723-228784311	HepG2	liver:	n/a	chr1:228783943-228783952
17	YY1	chr1:228783692-228784298	H1-hESC	embryonic stem cell:	n/a	chr1:228783943-228783952
18	CEBPB	chr1:228783319-228784373	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:228782399-228784366	HepG2	liver:	n/a	n/a
20	SIN3A	chr1:228782544-228784269	H1-hESC	embryonic stem cell:	n/a	chr1:228783147-228783161
21	TCF7L2	chr1:228782502-228784333	HCT-116	colon:	n/a	n/a
22	POLR2A	chr1:228782424-228784404	H1-neurons	neurons:	n/a	n/a
23	MAX	chr1:228782410-228784286	HCT-116	colon:	n/a	chr1:228784239-228784249
24	MAX	chr1:228782435-228784396	A549	lung:	n/a	chr1:228784239-228784249
25	E2F6	chr1:228782917-228784392	A549	lung:	n/a	chr1:228783805-228783812 chr1:228783095-228783105 chr1:228783096-228783107 chr1:228783096-228783104 chr1:228783095-228783106 chr1:228783943-228783952 chr1:228783084-228783098 chr1:228783096-228783103 chr1:228783384-228783396 chr1:228783096-228783104
26	GATA3	chr1:228783147-228784396	SK-N-SH	brain:	n/a	n/a
27	YY1	chr1:228783292-228784288	SK-N-SH	brain:	n/a	chr1:228783943-228783952
28	TCF12	chr1:228782357-228784409	A549	lung:	n/a	n/a
29	MAX	chr1:228783016-228784285	SK-N-SH	brain:	n/a	chr1:228784239-228784249
30	MAX	chr1:228782434-228784273	SK-N-SH	brain:	n/a	chr1:228784239-228784249
31	MAX	chr1:228782409-228784383	Hela-S3	cervix:	n/a	chr1:228784239-228784249
32	MAX	chr1:228782921-228784384	A549	lung:	n/a	chr1:228784239-228784249

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169454738..169455424-chr1:228783655..228784433,2	Hela-S3	cervix:
2	chr1:228782241..228785119-chr1:228785249..228788137,2	K562	blood:

Variant related genes	Relation type
RNA5S16	TF binding region
DUSP5P1	TF binding region
RNA5SP18	TF binding region
ENSG00000206878	TF binding region
RNA5S17	TF binding region
ENSG00000117479	Chromatin interaction
ENSG00000183929	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10916331	0.90[JPT][hapmap]
rs10916348	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs12044013	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12045742	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12046644	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12047219	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12161195	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12161347	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12563568	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1925715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1925723	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61825663	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61825664	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61827306	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827315	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61827317	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61827321	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6426509	0.81[JPT][hapmap]
rs6658934	0.84[AMR][1000 genomes]
rs6661618	0.84[AMR][1000 genomes]
rs6672815	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs6681216	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs942850	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	esv1828070	chr1:228758016-228793246	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228782400-228784400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:228782400-228784400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:228782400-228784400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr1:228782400-228784400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:228782400-228784400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:228782400-228784400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
9	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
10	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr1:228782400-228784400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
15	chr1:228782400-228784600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:228782400-228784600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:228782400-228784600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:228782400-228784600	Active TSS	A549	lung
19	chr1:228782400-228785000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:228782400-228785000	Active TSS	Hela-S3	cervix
21	chr1:228782600-228784400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
22	chr1:228782600-228784400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
23	chr1:228782600-228784400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
24	chr1:228782600-228784400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
25	chr1:228782600-228784400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
26	chr1:228782600-228784400	Flanking Active TSS	Right Ventricle	heart
27	chr1:228782600-228784800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:228782800-228784400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:228782800-228784400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr1:228783000-228784400	Active TSS	NHDF-Ad	bronchial
31	chr1:228783000-228784600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:228783200-228784400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr1:228783200-228784400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:228783200-228784400	Bivalent/Poised TSS	NHLF	lung
35	chr1:228783200-228784600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:228783400-228784400	Flanking Active TSS	Ovary	ovary
37	chr1:228783400-228784800	Bivalent Enhancer	Spleen	Spleen
38	chr1:228783600-228784400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:228783600-228784600	Bivalent/Poised TSS	Fetal Brain Female	brain
40	chr1:228783600-228784800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:228783800-228784400	Bivalent Enhancer	Fetal Brain Male	brain
42	chr1:228783800-228784600	Active TSS	HepG2	liver
43	chr1:228784000-228784400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
44	chr1:228784000-228784400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr1:228784000-228784400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr1:228784000-228784400	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:228784000-228784400	Bivalent Enhancer	Brain Substantia Nigra	brain
48	chr1:228784000-228784400	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
49	chr1:228784000-228784600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
50	chr1:228784000-228784800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood

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