Variant report

Variant	rs16860758
Chromosome Location	chr3:112990314-112990315
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	CTCF	chr3:112990180-112990330	SAEC	small airway:	n/a	n/a
2	CTCF	chr3:112990188-112990323	MCF-7	breast:	n/a	n/a
3	NFIC	chr3:112989978-112990633	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr3:112990225-112990314	NHEK	skin:	n/a	n/a
5	CTCF	chr3:112990260-112990410	BE2_C	brain:	n/a	n/a
6	CTCF	chr3:112990177-112990331	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10511323	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710894	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11717833	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11919134	0.83[AMR][1000 genomes]
rs11928342	0.94[AMR][1000 genomes]
rs12485329	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12492273	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494864	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12631733	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12638030	0.94[CHB][hapmap];0.80[JPT][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16860787	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2036282	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2201971	0.82[AMR][1000 genomes]
rs34284771	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3814398	0.83[CEU][hapmap];0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs3846046	0.84[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3856718	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3856719	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3856720	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4682131	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682132	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682478	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682479	1.00[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682480	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4682481	0.93[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682483	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73235142	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73235143	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73235147	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73235153	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7641410	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs775222	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 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	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
3	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
4	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
6	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:112981200-112991000	Genic enhancers	Fetal Muscle Leg	muscle
9	chr3:112981600-112994400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:112982800-112993600	Weak transcription	HMEC	breast
11	chr3:112983800-112995000	Weak transcription	Lung	lung
12	chr3:112984000-112994400	Weak transcription	HSMMtube	muscle
13	chr3:112984200-112993600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:112984200-112994400	Weak transcription	HSMM	muscle
15	chr3:112984600-112991200	Weak transcription	Brain Germinal Matrix	brain
16	chr3:112984600-112993400	Weak transcription	Fetal Brain Male	brain
17	chr3:112984800-112992400	Weak transcription	Fetal Thymus	thymus
18	chr3:112984800-112993000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:112985400-112993600	Strong transcription	Fetal Lung	lung
22	chr3:112986200-112990400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr3:112986200-112994200	Strong transcription	Ovary	ovary
24	chr3:112986400-112993000	Strong transcription	Fetal Intestine Small	intestine
25	chr3:112986400-112994600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:112986600-112990600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:112986600-112993800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:112987200-112990600	Strong transcription	Fetal Intestine Large	intestine
29	chr3:112987200-112993400	Strong transcription	Fetal Stomach	stomach
30	chr3:112987200-112994400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:112987400-112991200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:112987800-112991200	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
34	chr3:112988000-112991000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:112988000-112992200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:112988000-112993600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:112988000-112993800	Weak transcription	Brain Angular Gyrus	brain
38	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr3:112988200-112992600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:112988200-112993400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:112988200-112993600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:112988200-112993800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:112988200-112994200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:112988200-112994200	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:112988200-112994600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:112988400-112991600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:112988400-112994000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:112988400-112994600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
50	chr3:112989000-112990400	Genic enhancers	Colon Smooth Muscle	Colon

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