Variant report

Variant	rs2046376
Chromosome Location	chr3:47469034-47469035
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	POLR2A	chr3:47468646-47469225	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
SCAP	TF binding region

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13080450	1.00[CHB][hapmap]
rs2170814	1.00[CHB][hapmap]
rs2270569	1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs3772406	1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]

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	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv236116	chr3:47469033-47469034	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47441000-47476800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:47456000-47473000	Strong transcription	Thymus	Thymus
4	chr3:47459600-47470000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr3:47460400-47470400	Strong transcription	NHEK	skin
6	chr3:47461800-47478800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr3:47463000-47469800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:47463000-47470200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:47463000-47470600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:47463200-47470200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:47463200-47470400	Strong transcription	Brain Germinal Matrix	brain
13	chr3:47463200-47470600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:47463200-47472800	Weak transcription	HUVEC	blood vessel
15	chr3:47463200-47472800	Weak transcription	NHDF-Ad	bronchial
16	chr3:47463200-47473000	Weak transcription	NH-A	brain
17	chr3:47463200-47474400	Weak transcription	Fetal Kidney	kidney
18	chr3:47463400-47470200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:47463400-47470200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:47463400-47470400	Strong transcription	Placenta	Placenta
21	chr3:47463400-47470600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:47463400-47471200	Weak transcription	Fetal Brain Male	brain
23	chr3:47463400-47475400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:47463400-47477600	Strong transcription	Fetal Thymus	thymus
25	chr3:47463400-47484600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:47463600-47470200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:47463600-47470400	Strong transcription	Brain Anterior Caudate	brain
28	chr3:47463600-47471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:47463600-47472400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:47463600-47476800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:47463600-47476800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:47463600-47484800	Strong transcription	Primary T cells from cord blood	blood
33	chr3:47463800-47470000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:47463800-47470400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:47463800-47471400	Strong transcription	Fetal Brain Female	brain
36	chr3:47463800-47472800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:47463800-47473000	Strong transcription	Fetal Stomach	stomach
38	chr3:47463800-47476800	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:47463800-47479400	Weak transcription	A549	lung
40	chr3:47464000-47470400	Strong transcription	Brain Hippocampus Middle	brain
41	chr3:47464000-47470800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:47464000-47474800	Weak transcription	HSMM	muscle
43	chr3:47464000-47476600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr3:47464000-47476800	Strong transcription	Dnd41	blood
45	chr3:47464000-47484200	Weak transcription	Right Atrium	heart
46	chr3:47464200-47470200	Strong transcription	Brain Cingulate Gyrus	brain
47	chr3:47464200-47470200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr3:47464200-47470200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr3:47464400-47470000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:47464400-47470000	Strong transcription	Esophagus	oesophagus

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