Variant report

Variant	rs56075614
Chromosome Location	chr3:98538817-98538818
allele	G/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	POLR2A	chr3:98537958-98539024	U87	brain:	n/a	n/a
2	POLR2A	chr3:98532422-98540691	U87	brain:	n/a	n/a
3	POLR2A	chr3:98531678-98540691	U87	brain:	n/a	n/a
4	POLR2A	chr3:98530977-98539024	U87	brain:	n/a	n/a
5	MYC	chr3:98538711-98538837	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10433438	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10935518	0.91[EUR][1000 genomes]
rs11716579	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11914715	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11916285	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440154	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16840260	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16846347	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17210963	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17278047	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17852693	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1822017	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1827158	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278599	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772100	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55650073	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55662129	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55730510	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55988144	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56290036	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56322058	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6440159	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805605	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73136038	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73136045	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136048	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136057	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136060	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138004	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138027	0.97[EUR][1000 genomes]
rs73138030	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73138048	0.93[EUR][1000 genomes]
rs73138053	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138055	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138058	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73138063	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73138082	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73140009	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7614892	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7644946	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8179927	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 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	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
3	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
4	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:98524200-98544200	Strong transcription	HSMM	muscle
7	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
8	chr3:98526200-98543200	Weak transcription	Lung	lung
9	chr3:98526400-98539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:98526400-98539400	Weak transcription	Fetal Brain Male	brain
11	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
13	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
14	chr3:98526600-98539000	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:98526600-98540000	Weak transcription	Fetal Thymus	thymus
16	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:98528600-98543600	Strong transcription	NHEK	skin
22	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:98529000-98540000	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:98529400-98539000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:98530400-98542000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:98530800-98542600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:98532400-98541200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
30	chr3:98532800-98541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:98534000-98545000	Weak transcription	Ovary	ovary
32	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:98534200-98539800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:98534200-98542800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:98534400-98545600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:98534600-98544200	Strong transcription	HMEC	breast
38	chr3:98534600-98545600	Weak transcription	Fetal Intestine Small	intestine
39	chr3:98534800-98539600	Genic enhancers	A549	lung
40	chr3:98535200-98540200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:98535400-98541800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:98535400-98542600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr3:98535400-98543800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:98535600-98541600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:98536000-98540400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:98536000-98542000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:98536000-98542800	Strong transcription	NH-A	brain
48	chr3:98536000-98552600	Weak transcription	Pancreas	Pancrea
49	chr3:98536200-98542600	Weak transcription	Fetal Intestine Large	intestine
50	chr3:98536200-98542600	Weak transcription	Fetal Stomach	stomach

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