Variant report

Variant	rs56116734
Chromosome Location	chr3:28383717-28383718
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28378547..28380122-chr3:28381729..28384245,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12054402	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680906	0.81[ASN][1000 genomes]
rs55954817	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
2	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
3	chr3:28349800-28389400	Weak transcription	Gastric	stomach
4	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
5	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:28360400-28383800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:28360400-28387400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
9	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
11	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
12	chr3:28365400-28383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:28365400-28389400	Weak transcription	Lung	lung
14	chr3:28366000-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
16	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:28367000-28384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:28367000-28388800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:28367200-28384000	Weak transcription	Fetal Heart	heart
21	chr3:28367200-28387800	Weak transcription	Fetal Brain Male	brain
22	chr3:28367200-28388800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
24	chr3:28367400-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:28368400-28387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:28368400-28388800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:28370200-28384000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:28372400-28384200	Weak transcription	A549	lung
29	chr3:28372400-28388400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr3:28373400-28388400	Weak transcription	Stomach Mucosa	stomach
31	chr3:28374000-28387800	Weak transcription	Brain Germinal Matrix	brain
32	chr3:28377200-28384000	Weak transcription	Right Ventricle	heart
33	chr3:28377200-28384400	Weak transcription	Small Intestine	intestine
34	chr3:28377400-28383800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:28377400-28383800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr3:28377800-28387600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:28377800-28387600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:28377800-28388600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:28377800-28389200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:28378400-28389400	Weak transcription	Ovary	ovary
41	chr3:28378800-28384200	Weak transcription	Fetal Intestine Small	intestine
42	chr3:28378800-28387400	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:28379000-28389600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:28379200-28383800	Weak transcription	Fetal Kidney	kidney
45	chr3:28379200-28386400	Weak transcription	Brain Anterior Caudate	brain
46	chr3:28379200-28387800	Weak transcription	Psoas Muscle	Psoas
47	chr3:28379200-28388200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:28379400-28384600	Weak transcription	Primary T cells from cord blood	blood
49	chr3:28379400-28388800	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:28379600-28386400	Weak transcription	Rectal Mucosa Donor 31	rectum

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