Variant report

Variant	rs10478424
Chromosome Location	chr5:118789020-118789021
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	GATA3	chr5:118788462-118789113	MCF-7	breast:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637 chr5:118788627-118788635
2	ZMIZ1	chr5:118787887-118789066	K562	blood:	n/a	n/a
3	POLR2A	chr5:118788015-118789066	K562	blood:	n/a	n/a
4	TCF7L2	chr5:118788043-118789030	Hela-S3	cervix:	n/a	n/a
5	CREB1	chr5:118787864-118789123	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:118787809-118789070	HepG2	liver:	n/a	n/a
7	GATA1	chr5:118788092-118789851	PBDE	blood:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637
8	NR3C1	chr5:118788677-118789045	A549	lung:	n/a	chr5:118788889-118788907 chr5:118788885-118788911 chr5:118788888-118788909 chr5:118788885-118788911 chr5:118788891-118788906 chr5:118788898-118788905
9	HA-E2F1	chr5:118787771-118789082	MCF-7	breast:	n/a	chr5:118788719-118788729
10	POLR2A	chr5:118787811-118789208	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr5:118787968-118789042	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF2	chr5:118787920-118789040	H1-hESC	embryonic stem cell:	n/a	chr5:118788712-118788728
13	SIN3AK20	chr5:118787715-118789176	MCF-7	breast:	n/a	n/a
14	MYBL2	chr5:118787838-118789044	HepG2	liver:	n/a	n/a
15	RCOR1	chr5:118787989-118789115	K562	blood:	n/a	n/a
16	POLR2A	chr5:118787933-118789335	MCF10A-Er-Src	breast:	n/a	n/a
17	JUND	chr5:118787940-118789027	K562	blood:	n/a	n/a
18	MAX	chr5:118787887-118789037	Hela-S3	cervix:	n/a	n/a
19	KAP1	chr5:118787129-118789033	HEK293	kidney:	n/a	n/a
20	NR2F2	chr5:118787530-118789239	K562	blood:	n/a	n/a
21	GATA2	chr5:118788091-118789068	SH-SY5Y	brain:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637 chr5:118788623-118788637
22	MYBL2	chr5:118787960-118789136	HepG2	liver:	n/a	n/a
23	HNF4G	chr5:118788123-118789045	HepG2	liver:	n/a	chr5:118788568-118788583
24	TEAD4	chr5:118787896-118789226	K562	blood:	n/a	n/a
25	MBD4	chr5:118788141-118789089	HepG2	liver:	n/a	n/a
26	TEAD4	chr5:118788358-118789183	HepG2	liver:	n/a	n/a
27	UBTF	chr5:118788109-118789053	K562	blood:	n/a	n/a
28	POLR2A	chr5:118788062-118790211	HepG2	liver:	n/a	n/a
29	NR2F2	chr5:118788780-118789424	MCF-7	breast:	n/a	n/a
30	GATA2	chr5:118788406-118789022	HUVEC	blood vessel:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637 chr5:118788623-118788637
31	HDAC2	chr5:118787969-118789099	HepG2	liver:	n/a	chr5:118788627-118788636
32	POLR2A	chr5:118787604-118790194	HepG2	liver:	n/a	n/a
33	MYC	chr5:118787930-118789056	K562	blood:	n/a	n/a
34	MAZ	chr5:118787989-118789080	HepG2	liver:	n/a	n/a
35	RXRA	chr5:118788259-118789021	HepG2	liver:	n/a	chr5:118788840-118788847
36	RCOR1	chr5:118787848-118789079	K562	blood:	n/a	n/a
37	POLR2A	chr5:118788026-118789088	HepG2	liver:	n/a	n/a
38	CEBPB	chr5:118788165-118789114	HepG2	liver:	n/a	chr5:118788595-118788608 chr5:118788597-118788608 chr5:118788595-118788606
39	POLR2A	chr5:118788901-118789053	Hela-S3	cervix:	n/a	n/a
40	EP300	chr5:118788205-118789095	HepG2	liver:	n/a	n/a
41	HCFC1	chr5:118787556-118789172	Hela-S3	cervix:	n/a	n/a
42	HEY1	chr5:118787825-118789039	HepG2	liver:	n/a	n/a
43	HEY1	chr5:118787880-118789057	HepG2	liver:	n/a	n/a
44	SMARCB1	chr5:118788071-118789065	Hela-S3	cervix:	n/a	chr5:118788098-118788107
45	FOXA2	chr5:118788446-118789024	HepG2	liver:	n/a	n/a
46	NR3C1	chr5:118788709-118789078	A549	lung:	n/a	chr5:118788889-118788907 chr5:118788885-118788911 chr5:118788888-118788909 chr5:118788885-118788911 chr5:118788891-118788906 chr5:118788898-118788905

No.	Distal block	Cell Line	Cell type
1	chr5:118323861..118326778-chr5:118787539..118789741,2	MCF-7	breast:
2	chr5:118788483..118791355-chr5:118802793..118805177,3	K562	blood:
3	chr5:118787302..118789344-chr5:118814419..118817189,2	K562	blood:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000133835	Chromatin interaction
ENSG00000239084	Chromatin interaction
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10059654	0.88[ASN][1000 genomes]
rs11205	0.83[CHB][hapmap]
rs11241507	0.82[CHB][hapmap]
rs1155777	0.82[CHB][hapmap]
rs11749784	0.81[MEX][hapmap]
rs150938	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs257969	0.82[JPT][hapmap]
rs257985	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2914210	0.83[CHB][hapmap]
rs3797368	0.86[CHB][hapmap]
rs3797372	0.83[CHB][hapmap]
rs6897978	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];1.00[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	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv4974	chr5:118750259-118795376	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118787400-118789200	Active TSS	Brain Hippocampus Middle	brain
2	chr5:118787400-118789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:118787600-118789200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr5:118787600-118789200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:118787600-118789200	Active TSS	Brain Substantia Nigra	brain
6	chr5:118787600-118789200	Active TSS	NHEK	skin
7	chr5:118787800-118789200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:118787800-118789200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:118787800-118789200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:118787800-118789200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr5:118787800-118789200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:118787800-118789200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:118787800-118789200	Active TSS	Colonic Mucosa	Colon
14	chr5:118787800-118789200	Active TSS	Fetal Stomach	stomach
15	chr5:118787800-118789200	Active TSS	Left Ventricle	heart
16	chr5:118787800-118789200	Active TSS	Pancreas	Pancrea
17	chr5:118787800-118789200	Active TSS	Thymus	Thymus
18	chr5:118787800-118789200	Active TSS	HSMM	muscle
19	chr5:118787800-118789200	Active TSS	NHDF-Ad	bronchial
20	chr5:118787800-118789200	Active TSS	NHLF	lung
21	chr5:118787800-118789400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr5:118787800-118789400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr5:118787800-118789400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:118787800-118789400	Active TSS	HSMMtube	muscle
25	chr5:118787800-118789400	Active TSS	NH-A	brain
26	chr5:118787800-118790000	Active TSS	Fetal Brain Male	brain
27	chr5:118787800-118790200	Active TSS	Aorta	Aorta
28	chr5:118788000-118789200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:118788000-118789200	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr5:118788000-118789200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:118788000-118789200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr5:118788000-118789200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr5:118788000-118789200	Active TSS	Colon Smooth Muscle	Colon
34	chr5:118788000-118789200	Active TSS	Right Ventricle	heart
35	chr5:118788000-118789200	Active TSS	GM12878-XiMat	blood
36	chr5:118788000-118789400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr5:118788000-118789400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:118788000-118789400	Active TSS	Psoas Muscle	Psoas
39	chr5:118788000-118789600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr5:118788000-118789600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr5:118788000-118789800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr5:118788000-118790000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:118788000-118790000	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr5:118788200-118789200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr5:118788200-118789200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:118788200-118789200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:118788200-118789200	Active TSS	Gastric	stomach
48	chr5:118788400-118789200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr5:118788400-118789200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
50	chr5:118788400-118789200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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