Variant report

Variant	rs11860416
Chromosome Location	chr16:73050576-73050577
allele	C/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	CHD2	chr16:73049885-73050747	GM12878	blood:	n/a	n/a
2	NFIC	chr16:73049803-73051046	GM12878	blood:	n/a	n/a
3	POLR2A	chr16:73050521-73050786	GM12891	blood:	n/a	n/a
4	RUNX3	chr16:73049804-73050835	GM12878	blood:	n/a	n/a
5	MTA3	chr16:73049898-73050838	GM12878	blood:	n/a	n/a
6	FOXM1	chr16:73049909-73050859	GM12878	blood:	n/a	n/a
7	RCOR1	chr16:73049885-73050747	GM12878	blood:	n/a	n/a
8	STAT1	chr16:73050025-73050628	GM12878	blood:	n/a	chr16:73050206-73050214
9	POLR2A	chr16:73049740-73050623	HepG2	liver:	n/a	n/a
10	EP300	chr16:73049941-73050590	GM12878	blood:	n/a	chr16:73050448-73050462 chr16:73050450-73050464
11	NFIC	chr16:73049804-73050643	HepG2	liver:	n/a	n/a
12	MEF2C	chr16:73049887-73050825	GM12878	blood:	n/a	n/a
13	BATF	chr16:73049904-73050765	GM12878	blood:	n/a	n/a
14	SP1	chr16:73049897-73050744	GM12878	blood:	n/a	n/a
15	BHLHE40	chr16:73049881-73050937	GM12878	blood:	n/a	n/a
16	SP1	chr16:73049925-73050719	GM12878	blood:	n/a	n/a
17	MEF2A	chr16:73049948-73050810	GM12878	blood:	n/a	n/a
18	SPI1	chr16:73049481-73050631	GM12878	blood:	n/a	chr16:73050114-73050123 chr16:73050113-73050126 chr16:73049661-73049674 chr16:73050112-73050125
19	RUNX3	chr16:73049719-73050797	GM12878	blood:	n/a	n/a
20	ATF2	chr16:73049866-73050759	GM12878	blood:	n/a	n/a
21	CEBPB	chr16:73049250-73050886	HCT-116	colon:	n/a	chr16:73049772-73049785 chr16:73049774-73049783 chr16:73049772-73049783 chr16:73049774-73049785
22	FOSL1	chr16:73050284-73050869	HCT-116	colon:	n/a	n/a
23	BCL11A	chr16:73049874-73050673	GM12878	blood:	n/a	n/a
24	STAT5A	chr16:73049999-73050774	GM12878	blood:	n/a	chr16:73050206-73050214
25	SP1	chr16:73050222-73050956	HCT-116	colon:	n/a	n/a
26	STAT3	chr16:73049919-73050632	GM12878	blood:	n/a	chr16:73050206-73050214
27	RELA	chr16:73049892-73050704	GM19099	blood:	n/a	n/a
28	FOS	chr16:73050422-73050632	MCF10A-Er-Src	breast:	n/a	n/a
29	EP300	chr16:73049864-73050780	GM12878	blood:	n/a	chr16:73050448-73050462 chr16:73050450-73050464
30	BCLAF1	chr16:73049883-73050804	GM12878	blood:	n/a	n/a
31	TBL1XR1	chr16:73049762-73050940	GM12878	blood:	n/a	n/a
32	ZNF143	chr16:73049822-73050817	GM12878	blood:	n/a	n/a
33	IKZF1	chr16:73049816-73050865	GM12878	blood:	n/a	n/a
34	NFIC	chr16:73049917-73050782	GM12878	blood:	n/a	n/a
35	CEBPB	chr16:73049210-73050944	HCT-116	colon:	n/a	chr16:73049772-73049785 chr16:73049774-73049783 chr16:73049772-73049783 chr16:73049774-73049785
36	EBF1	chr16:73049784-73050975	GM12878	blood:	n/a	chr16:73050775-73050786
37	BCLAF1	chr16:73050283-73050806	GM12878	blood:	n/a	n/a
38	ATF2	chr16:73049851-73050830	GM12878	blood:	n/a	n/a
39	ARID3A	chr16:73049652-73050667	HepG2	liver:	n/a	n/a
40	MTA3	chr16:73049861-73050938	GM12878	blood:	n/a	n/a
41	WRNIP1	chr16:73050567-73050821	GM12878	blood:	n/a	n/a
42	IRF4	chr16:73050254-73050689	GM12878	blood:	n/a	n/a
43	MXI1	chr16:73049923-73050744	GM12878	blood:	n/a	n/a
44	EP300	chr16:73049887-73050870	GM12878	blood:	n/a	chr16:73050448-73050462 chr16:73050450-73050464
45	CEBPB	chr16:73049862-73050824	GM12878	blood:	n/a	n/a
46	NFATC1	chr16:73049800-73050799	GM12878	blood:	n/a	n/a
47	BATF	chr16:73050293-73050711	GM12878	blood:	n/a	n/a
48	MEF2A	chr16:73049911-73050845	GM12878	blood:	n/a	n/a
49	IRF4	chr16:73049862-73050829	GM12878	blood:	n/a	n/a
50	SPI1	chr16:73049814-73050606	GM12891	blood:	n/a	chr16:73050114-73050123 chr16:73050113-73050126 chr16:73050112-73050125

No.	Distal block	Cell Line	Cell type
1	chr16:73050031..73052152-chr16:73076520..73078945,2	MCF-7	breast:
2	chr16:73048726..73050990-chr16:73083446..73086063,2	MCF-7	breast:
3	chr16:73050220..73052813-chr16:73058452..73060426,2	MCF-7	breast:
4	chr16:73049713..73052075-chr16:73126664..73128692,2	MCF-7	breast:
5	chr16:73048377..73052863-chr16:73053930..73057468,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272330	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11075959	1.00[CEU][hapmap]
rs11860964	1.00[MEX][hapmap]
rs12373097	0.93[JPT][hapmap]
rs28688024	0.90[EUR][1000 genomes]
rs55989215	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58876449	0.82[ASN][1000 genomes]
rs6416746	0.85[CHD][hapmap]
rs6499604	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6499605	1.00[CEU][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs7203164	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73594757	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74030209	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74030210	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906898	chr16:73017684-73128146	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:73035600-73053000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr16:73044600-73050800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:73044600-73052600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr16:73044600-73052800	Weak transcription	Spleen	Spleen
5	chr16:73044600-73053000	Weak transcription	Fetal Stomach	stomach
6	chr16:73044600-73053200	Weak transcription	Brain Angular Gyrus	brain
7	chr16:73044800-73052200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr16:73044800-73052600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:73044800-73053000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr16:73046200-73050600	Weak transcription	Aorta	Aorta
11	chr16:73047200-73052800	Weak transcription	Fetal Muscle Leg	muscle
12	chr16:73047800-73051800	Enhancers	Pancreas	Pancrea
13	chr16:73048000-73052600	Weak transcription	Osteobl	bone
14	chr16:73048800-73051600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr16:73049000-73050800	Enhancers	Fetal Kidney	kidney
16	chr16:73049000-73051200	Enhancers	Adipose Nuclei	Adipose
17	chr16:73049000-73051800	Enhancers	Liver	Liver
18	chr16:73049000-73051800	Enhancers	Lung	lung
19	chr16:73049000-73051800	Enhancers	Stomach Mucosa	stomach
20	chr16:73049000-73052000	Enhancers	Fetal Intestine Large	intestine
21	chr16:73049000-73052000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr16:73049200-73050600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr16:73049200-73050600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr16:73049200-73050800	Enhancers	NHEK	skin
25	chr16:73049200-73051000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:73049400-73050800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr16:73049400-73050800	Flanking Active TSS	HepG2	liver
28	chr16:73049400-73051000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr16:73049400-73051000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr16:73049400-73051200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:73049400-73051200	Enhancers	Primary hematopoietic stem cells	blood
32	chr16:73049400-73051800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:73049400-73051800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr16:73049400-73051800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr16:73049400-73052000	Enhancers	Fetal Lung	lung
36	chr16:73049400-73069200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr16:73049600-73051000	Flanking Active TSS	GM12878-XiMat	blood
38	chr16:73049600-73051400	Enhancers	Small Intestine	intestine
39	chr16:73049600-73051600	Enhancers	Gastric	stomach
40	chr16:73049600-73051800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr16:73049600-73051800	Enhancers	Brain Hippocampus Middle	brain
42	chr16:73049600-73051800	Enhancers	Esophagus	oesophagus
43	chr16:73049600-73051800	Enhancers	Left Ventricle	heart
44	chr16:73049600-73051800	Enhancers	Right Ventricle	heart
45	chr16:73049600-73052000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr16:73049600-73056800	Enhancers	Psoas Muscle	Psoas
47	chr16:73049800-73050800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr16:73049800-73051000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr16:73049800-73051000	Enhancers	HSMMtube	muscle
50	chr16:73049800-73051000	Enhancers	NH-A	brain

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