Variant report

Variant	rs73407856
Chromosome Location	chr15:55489929-55489930
allele	A/G
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	USF2	chr15:55489758-55490054	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:55488856-55489990	HCT-116	colon:	n/a	n/a
3	MAFK	chr15:55488354-55489951	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr15:55487285-55490596	SK-N-SH	brain:	n/a	n/a
5	RCOR1	chr15:55488885-55490002	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:55488481-55489956	K562	blood:	n/a	n/a
7	TBP	chr15:55489891-55489954	H1-hESC	embryonic stem cell:	n/a	n/a
8	EBF1	chr15:55488548-55489961	GM12878	blood:	n/a	chr15:55488881-55488892 chr15:55488880-55488893 chr15:55488882-55488892 chr15:55488882-55488891
9	HCFC1	chr15:55488000-55490587	Hela-S3	cervix:	n/a	n/a
10	RCOR1	chr15:55487915-55490059	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr15:55488208-55490000	GM12878	blood:	n/a	n/a
12	GTF2F1	chr15:55488182-55489965	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr15:55488556-55489932	K562	blood:	n/a	n/a
14	SIN3A	chr15:55488167-55489977	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBL1XR1	chr15:55488239-55489932	GM12878	blood:	n/a	n/a
16	NRF1	chr15:55488468-55489970	SK-N-SH	brain:	n/a	chr15:55488843-55488850 chr15:55489285-55489299 chr15:55489285-55489296
17	JUND	chr15:55488341-55489986	Hela-S3	cervix:	n/a	n/a
18	UBTF	chr15:55488527-55490068	K562	blood:	n/a	n/a
19	MYC	chr15:55488350-55489998	K562	blood:	n/a	n/a
20	POLR2A	chr15:55488431-55489966	GM18505	blood:	n/a	n/a
21	POLR2A	chr15:55488601-55489959	GM19099	blood:	n/a	n/a
22	REST	chr15:55488377-55489932	H1-neurons	neurons:	n/a	n/a
23	RCOR1	chr15:55488648-55490074	K562	blood:	n/a	n/a
24	POLR2A	chr15:55488340-55489977	Hela-S3	cervix:	n/a	n/a
25	PML	chr15:55488448-55490048	GM12878	blood:	n/a	n/a
26	ZNF143	chr15:55488843-55489938	GM12878	blood:	n/a	chr15:55489714-55489723 chr15:55489712-55489721
27	TBP	chr15:55488066-55490006	Hela-S3	cervix:	n/a	n/a
28	CUX1	chr15:55489817-55490245	K562	blood:	n/a	chr15:55490088-55490099
29	POLR2A	chr15:55488355-55490020	GM12891	blood:	n/a	n/a
30	KAP1	chr15:55488616-55489985	HEK293	kidney:	n/a	n/a
31	ELK1	chr15:55488823-55490008	GM12878	blood:	n/a	chr15:55489154-55489163 chr15:55489154-55489163
32	POLR2A	chr15:55488530-55489979	Raji	blood:	n/a	n/a
33	POLR2A	chr15:55488547-55489982	K562	blood:	n/a	n/a
34	TBL1XR1	chr15:55489799-55490143	K562	blood:	n/a	n/a
35	TAL1	chr15:55488730-55489971	K562	blood:	n/a	n/a
36	ZMIZ1	chr15:55489804-55490093	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55484699..55490442-chr15:55579270..55584640,8	K562	blood:
2	chr15:55489042..55491644-chr15:55640711..55643190,2	K562	blood:
3	chr15:55489860..55492561-chr15:55500870..55502505,2	K562	blood:
4	chr15:55488451..55490602-chr15:55640573..55642962,2	MCF-7	breast:
5	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
6	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:

Variant related genes	Relation type
RSL24D1	TF binding region
ENSG00000069943	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000259669	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12324612	1.00[EUR][1000 genomes]
rs28458789	1.00[EUR][1000 genomes]
rs28495958	1.00[EUR][1000 genomes]
rs60243408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7169189	1.00[EUR][1000 genomes]
rs73407829	1.00[EUR][1000 genomes]
rs73407831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407835	1.00[EUR][1000 genomes]
rs73407844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73407873	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73409838	1.00[EUR][1000 genomes]
rs73419725	1.00[EUR][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	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55485600-55490600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:55486600-55490000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr15:55486800-55490000	Active TSS	Psoas Muscle	Psoas
4	chr15:55487000-55490000	Active TSS	NHLF	lung
5	chr15:55487200-55490000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:55487200-55490200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:55487400-55490000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr15:55487400-55490200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr15:55487400-55490200	Active TSS	Right Atrium	heart
10	chr15:55487600-55490000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:55487600-55490000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:55487600-55490000	Active TSS	Fetal Brain Female	brain
13	chr15:55487600-55490200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:55487600-55490400	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr15:55487800-55490000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:55487800-55490000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:55487800-55490000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:55487800-55490000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:55487800-55490000	Active TSS	Fetal Intestine Small	intestine
20	chr15:55487800-55490000	Active TSS	Ovary	ovary
21	chr15:55487800-55490000	Active TSS	HSMMtube	muscle
22	chr15:55487800-55490200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:55487800-55490200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr15:55487800-55490200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr15:55487800-55490200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:55487800-55490200	Active TSS	Right Ventricle	heart
27	chr15:55487800-55490400	Active TSS	K562	blood
28	chr15:55488000-55490000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr15:55488000-55490000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr15:55488000-55490000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:55488000-55490000	Active TSS	Primary T cells fromperipheralblood	blood
32	chr15:55488000-55490000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr15:55488000-55490000	Active TSS	Brain Anterior Caudate	brain
34	chr15:55488000-55490000	Active TSS	Fetal Intestine Large	intestine
35	chr15:55488000-55490000	Active TSS	Fetal Muscle Trunk	muscle
36	chr15:55488000-55490000	Active TSS	Left Ventricle	heart
37	chr15:55488000-55490000	Active TSS	HSMM	muscle
38	chr15:55488000-55490000	Active TSS	NH-A	brain
39	chr15:55488000-55490200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:55488000-55490200	Active TSS	Fetal Muscle Leg	muscle
41	chr15:55488000-55490200	Active TSS	GM12878-XiMat	blood
42	chr15:55488000-55490200	Active TSS	HMEC	breast
43	chr15:55488000-55490400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:55488000-55490600	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr15:55488200-55490000	Active TSS	Brain Hippocampus Middle	brain
46	chr15:55488200-55490000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr15:55488200-55490000	Active TSS	Stomach Mucosa	stomach
48	chr15:55488200-55490000	Active TSS	A549	lung
49	chr15:55488200-55490200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr15:55488200-55490200	Active TSS	Duodenum Smooth Muscle	Duodenum

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