Variant report

Variant	rs71316249
Chromosome Location	chr3:20150360-20150361
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	GATA3	chr3:20150247-20151059	MCF-7	breast:	n/a	n/a
2	GATA3	chr3:20150299-20150985	MCF-7	breast:	n/a	n/a
3	GATA3	chr3:20150335-20150775	T-47D	breast:	n/a	n/a
4	GATA3	chr3:20150066-20151130	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr3:20150329-20151104	MCF-7	breast:	n/a	n/a
6	SIN3AK20	chr3:20150344-20150999	MCF-7	breast:	n/a	n/a
7	JUND	chr3:20150339-20150951	MCF-7	breast:	n/a	n/a
8	TCF12	chr3:20150348-20150907	MCF-7	breast:	n/a	n/a
9	HDAC2	chr3:20150313-20150942	MCF-7	breast:	n/a	n/a
10	FOXA2	chr3:20150321-20150636	A549	lung:	n/a	n/a

Variant related genes	Relation type
KAT2B	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11713069	1.00[ASN][1000 genomes]
rs13066876	1.00[ASN][1000 genomes]
rs13066923	1.00[ASN][1000 genomes]
rs13069629	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095743	1.00[ASN][1000 genomes]
rs13096876	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097157	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097409	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098588	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627750	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17627906	0.83[ASN][1000 genomes]
rs17627936	0.83[ASN][1000 genomes]
rs17678713	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17796904	1.00[ASN][1000 genomes]
rs17804451	1.00[ASN][1000 genomes]
rs34204839	1.00[ASN][1000 genomes]
rs34515517	1.00[ASN][1000 genomes]
rs34572705	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35424474	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632245	1.00[ASN][1000 genomes]
rs35645247	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35659955	1.00[ASN][1000 genomes]
rs35776229	1.00[ASN][1000 genomes]
rs35841175	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36029475	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3960789	1.00[ASN][1000 genomes]
rs41285061	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241545	1.00[ASN][1000 genomes]
rs4858156	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858171	1.00[ASN][1000 genomes]
rs4858751	1.00[ASN][1000 genomes]
rs4858752	1.00[ASN][1000 genomes]
rs4858755	1.00[ASN][1000 genomes]
rs4858763	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858765	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858768	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55812129	0.83[ASN][1000 genomes]
rs71316246	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71316248	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised 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	17 gene(s)	inside rSNPs	diseases
7	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	17 gene(s)	inside rSNPs	diseases
9	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised 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	18 gene(s)	inside rSNPs	diseases
13	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:20131800-20153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:20132800-20152400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:20137400-20156600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:20137600-20153000	Weak transcription	Spleen	Spleen
10	chr3:20137800-20153000	Weak transcription	Esophagus	oesophagus
11	chr3:20137800-20153000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:20137800-20153200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:20138000-20150400	Weak transcription	Fetal Intestine Large	intestine
14	chr3:20138000-20152800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:20138000-20153000	Weak transcription	Aorta	Aorta
16	chr3:20138000-20153000	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:20138800-20152600	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:20138800-20156400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:20139000-20152800	Weak transcription	Liver	Liver
20	chr3:20139000-20152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:20139000-20164000	Weak transcription	Small Intestine	intestine
22	chr3:20139800-20161000	Weak transcription	Fetal Intestine Small	intestine
23	chr3:20141000-20153200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:20141200-20153000	Weak transcription	Fetal Lung	lung
25	chr3:20141200-20167400	Weak transcription	HSMMtube	muscle
26	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:20141800-20153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:20141800-20153000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:20142200-20152600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
31	chr3:20143200-20150800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:20143200-20152800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:20143200-20152800	Weak transcription	Left Ventricle	heart
34	chr3:20143200-20153000	Weak transcription	Adipose Nuclei	Adipose
35	chr3:20143200-20153000	Weak transcription	Ovary	ovary
36	chr3:20143800-20152800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:20144600-20162000	Weak transcription	Fetal Heart	heart
38	chr3:20145400-20150800	Weak transcription	Fetal Thymus	thymus
39	chr3:20145800-20151800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:20146000-20156400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:20146000-20156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:20146200-20152800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:20146200-20153200	Weak transcription	Brain Anterior Caudate	brain
44	chr3:20146200-20154200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr3:20146200-20156400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:20146400-20152800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:20146400-20153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:20146400-20157600	Weak transcription	Fetal Brain Female	brain
49	chr3:20146400-20163400	Weak transcription	Brain Germinal Matrix	brain
50	chr3:20147400-20169600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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