Variant report

Variant	rs3936082
Chromosome Location	chr2:54777920-54777921
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	chr2:54777239-54777924	MCF-7	breast:	n/a	chr2:54777714-54777721 chr2:54777714-54777721 chr2:54777714-54777721 chr2:54777707-54777728

No.	Distal block	Cell Line	Cell type
1	chr2:54777010..54778863-chr2:54780329..54781851,2	MCF-7	breast:
2	chr2:54777753..54780191-chr2:54782738..54786905,5	K562	blood:
3	chr2:54763693..54765544-chr2:54775882..54778958,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234943	TF binding region
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10166179	1.00[EUR][1000 genomes]
rs10188600	1.00[EUR][1000 genomes]
rs1030601	1.00[EUR][1000 genomes]
rs11885098	1.00[EUR][1000 genomes]
rs11895933	0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13386997	1.00[EUR][1000 genomes]
rs13394958	1.00[EUR][1000 genomes]
rs13409783	1.00[EUR][1000 genomes]
rs13419870	1.00[EUR][1000 genomes]
rs4426561	1.00[ASN][1000 genomes]
rs4671950	0.85[YRI][hapmap]
rs56726104	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60616308	0.84[AMR][1000 genomes]
rs61332964	1.00[EUR][1000 genomes]
rs61743072	1.00[EUR][1000 genomes]
rs6545436	1.00[EUR][1000 genomes]
rs6545439	1.00[EUR][1000 genomes]
rs6729826	0.81[LWK][hapmap]
rs6753590	1.00[EUR][1000 genomes]
rs6753689	1.00[EUR][1000 genomes]
rs6756814	1.00[EUR][1000 genomes]
rs6757017	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs72918768	1.00[EUR][1000 genomes]
rs73932784	1.00[EUR][1000 genomes]
rs73934323	1.00[EUR][1000 genomes]
rs7559157	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv2731	chr2:54745069-54790057	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54758200-54778200	Weak transcription	Placenta	Placenta
2	chr2:54768200-54783800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:54770400-54782000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:54770600-54780200	Enhancers	Fetal Intestine Large	intestine
5	chr2:54771600-54783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:54772600-54778800	Enhancers	Brain Anterior Caudate	brain
7	chr2:54772600-54780200	Enhancers	Fetal Intestine Small	intestine
8	chr2:54773400-54784000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:54773400-54784000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:54773800-54782200	Weak transcription	Ovary	ovary
11	chr2:54774000-54779200	Enhancers	Duodenum Mucosa	Duodenum
12	chr2:54774000-54782400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:54774000-54782400	Weak transcription	Osteobl	bone
14	chr2:54774200-54778000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:54774200-54778000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:54774200-54779800	Weak transcription	NHDF-Ad	bronchial
17	chr2:54774600-54778000	Enhancers	Fetal Brain Male	brain
18	chr2:54774800-54778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:54774800-54778800	Enhancers	Brain Hippocampus Middle	brain
20	chr2:54774800-54781800	Weak transcription	Liver	Liver
21	chr2:54774800-54782400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:54775200-54778000	Enhancers	Fetal Brain Female	brain
23	chr2:54775400-54778600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:54775400-54778800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:54775400-54778800	Enhancers	Right Atrium	heart
26	chr2:54775400-54778800	Enhancers	Right Ventricle	heart
27	chr2:54775400-54778800	Enhancers	Small Intestine	intestine
28	chr2:54775400-54778800	Enhancers	Stomach Mucosa	stomach
29	chr2:54775400-54778800	Enhancers	HMEC	breast
30	chr2:54775400-54779000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:54775400-54779200	Genic enhancers	HepG2	liver
32	chr2:54775600-54779400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:54775800-54778000	Weak transcription	Spleen	Spleen
34	chr2:54775800-54778600	Enhancers	Brain Angular Gyrus	brain
35	chr2:54775800-54780600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr2:54775800-54782400	Weak transcription	HSMM	muscle
37	chr2:54776000-54778200	Enhancers	Left Ventricle	heart
38	chr2:54776200-54778000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:54776600-54778600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:54776600-54778800	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:54776600-54778800	Enhancers	NHEK	skin
42	chr2:54776800-54778000	Enhancers	HSMMtube	muscle
43	chr2:54776800-54778200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:54776800-54778400	Enhancers	Brain Substantia Nigra	brain
45	chr2:54776800-54778800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:54776800-54778800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr2:54776800-54779400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr2:54776800-54780200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:54776800-54780200	Enhancers	Pancreas	Pancrea
50	chr2:54777000-54778200	Genic enhancers	Fetal Lung	lung

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