Variant report

Variant	rs3771224
Chromosome Location	chr2:58460029-58460030
allele	C/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	STAT3	chr2:58460001-58460108	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:58444634..58446465-chr2:58458026..58460794,3	MCF-7	breast:
2	chr2:58459530..58463779-chr2:58463929..58469122,8	K562	blood:
3	chr2:58442380..58445315-chr2:58458064..58460897,2	MCF-7	breast:
4	chr2:58458402..58460893-chr2:58461273..58462970,2	MCF-7	breast:

Variant related genes	Relation type
FANCL	TF binding region
ENSG00000273063	Chromatin interaction
ENSG00000115392	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10172212	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1100190	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12477242	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2043890	0.84[EUR][1000 genomes]
rs3771221	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72618694	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72618695	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72618696	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs848285	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs848286	0.82[EUR][1000 genomes]
rs848287	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs848288	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs848289	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs848294	0.93[EUR][1000 genomes];0.80[ASN][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	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58391000-58467000	Weak transcription	HMEC	breast
2	chr2:58414000-58461400	Weak transcription	NHEK	skin
3	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr2:58437000-58460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:58440000-58465000	Weak transcription	Fetal Brain Male	brain
9	chr2:58440000-58467400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:58440600-58462000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:58440600-58467400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr2:58443400-58460400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:58443600-58462200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:58444200-58466200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:58448800-58464800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:58449400-58462400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:58450000-58466200	Weak transcription	HUVEC	blood vessel
18	chr2:58452000-58467400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:58452000-58467400	Weak transcription	NHLF	lung
20	chr2:58452600-58460600	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:58453800-58467400	Weak transcription	NHDF-Ad	bronchial
22	chr2:58454600-58466800	Weak transcription	HSMM	muscle
23	chr2:58454800-58460600	Weak transcription	Small Intestine	intestine
24	chr2:58454800-58462000	Weak transcription	K562	blood
25	chr2:58454800-58464400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:58454800-58464800	Weak transcription	Fetal Brain Female	brain
27	chr2:58454800-58466200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr2:58454800-58466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:58454800-58467400	Weak transcription	Primary B cells from cord blood	blood
30	chr2:58454800-58467400	Weak transcription	Fetal Thymus	thymus
31	chr2:58454800-58467400	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:58454800-58467400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:58454800-58467400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr2:58455000-58460400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:58455000-58462200	Weak transcription	Pancreas	Pancrea
36	chr2:58455000-58463000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:58455000-58465000	Weak transcription	Thymus	Thymus
38	chr2:58455000-58465400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:58455000-58466200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:58455000-58466200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:58455000-58466200	Weak transcription	Fetal Intestine Small	intestine
42	chr2:58455000-58466800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:58455000-58466800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:58455000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:58455000-58467400	Weak transcription	Fetal Stomach	stomach
46	chr2:58455000-58467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:58455000-58467600	Weak transcription	Left Ventricle	heart
48	chr2:58455000-58467600	Weak transcription	Ovary	ovary
49	chr2:58455000-58468000	Weak transcription	Gastric	stomach
50	chr2:58455000-58468000	Weak transcription	Spleen	Spleen

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