Variant report

Variant	rs3929128
Chromosome Location	chr2:55456266-55456267
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	POLR2A	chr2:55456140-55456323	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55346562..55348270-chr2:55453778..55456492,2	K562	blood:
2	chr2:55450659..55454031-chr2:55454419..55456893,3	K562	blood:

Variant related genes	Relation type
RPS27A	TF binding region
CLHC1	TF binding region
ENSG00000227799	Chromatin interaction
ENSG00000162994	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10183953	0.80[AFR][1000 genomes]
rs10439479	0.91[AFR][1000 genomes]
rs1437392	0.82[AFR][1000 genomes]
rs72916758	0.81[AFR][1000 genomes]
rs72918921	0.81[AFR][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	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55457200	Weak transcription	NHDF-Ad	bronchial
2	chr2:55451000-55457600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:55451000-55457600	Weak transcription	HMEC	breast
4	chr2:55451000-55457800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:55451000-55457800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:55451000-55458000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:55451000-55458000	Weak transcription	Osteobl	bone
8	chr2:55451000-55458400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:55451000-55458400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:55451000-55458400	Weak transcription	Aorta	Aorta
11	chr2:55451000-55458400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:55451000-55458400	Weak transcription	Fetal Brain Female	brain
13	chr2:55451000-55458600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:55451000-55458600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
17	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
18	chr2:55451200-55458400	Weak transcription	Fetal Kidney	kidney
19	chr2:55451200-55458400	Weak transcription	Fetal Lung	lung
20	chr2:55451400-55458400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:55451400-55458400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:55451400-55458600	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:55451400-55458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:55451600-55456600	Weak transcription	A549	lung
25	chr2:55451600-55457800	Weak transcription	Placenta	Placenta
26	chr2:55451800-55458400	Weak transcription	Brain Angular Gyrus	brain
27	chr2:55451800-55458600	Weak transcription	Fetal Intestine Small	intestine
28	chr2:55452200-55458600	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:55452400-55456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:55452400-55458400	Weak transcription	Fetal Stomach	stomach
31	chr2:55452600-55457600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:55452600-55458400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:55452600-55458400	Weak transcription	Brain Germinal Matrix	brain
34	chr2:55452800-55458400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:55453000-55457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:55453000-55458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:55453000-55458400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:55453000-55458600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:55453000-55458600	Weak transcription	Lung	lung
40	chr2:55453000-55458600	Weak transcription	Pancreas	Pancrea
41	chr2:55453000-55458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:55453200-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:55455000-55456800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:55455000-55458400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr2:55455000-55458400	Enhancers	HepG2	liver
46	chr2:55455200-55456600	Weak transcription	Fetal Intestine Large	intestine
47	chr2:55455400-55456800	Enhancers	Fetal Heart	heart
48	chr2:55455400-55456800	Strong transcription	Fetal Muscle Trunk	muscle
49	chr2:55455400-55457800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:55455400-55458400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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