Variant report

Variant	rs2291041
Chromosome Location	chr3:140947488-140947489
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	GATA3	chr3:140946492-140947554	SH-SY5Y	brain:	n/a	n/a
2	RAD21	chr3:140947183-140947535	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr3:140947360-140947510	A549	lung:	n/a	n/a
4	CTCF	chr3:140947209-140947636	MCF-7	breast:	n/a	n/a
5	CTCF	chr3:140947198-140947541	GM12878	blood:	n/a	n/a
6	EP300	chr3:140945422-140948945	SK-N-SH	brain:	n/a	chr3:140945945-140945959 chr3:140946516-140946530
7	RAD21	chr3:140947209-140947501	HepG2	liver:	n/a	n/a
8	FOXA2	chr3:140947216-140947694	HepG2	liver:	n/a	n/a
9	FOXA1	chr3:140947295-140947677	HepG2	liver:	n/a	chr3:140947500-140947515
10	HDAC2	chr3:140947260-140947758	MCF-7	breast:	n/a	n/a
11	RAD21	chr3:140947247-140947585	HepG2	liver:	n/a	n/a
12	FOXA1	chr3:140947229-140947684	HepG2	liver:	n/a	chr3:140947500-140947515
13	FOXA1	chr3:140947252-140947688	HepG2	liver:	n/a	chr3:140947500-140947515
14	FOXA1	chr3:140947270-140947646	HepG2	liver:	n/a	chr3:140947500-140947515
15	RAD21	chr3:140947206-140947669	MCF-7	breast:	n/a	n/a
16	FOXA1	chr3:140947235-140947715	T-47D	breast:	n/a	chr3:140947500-140947515
17	CEBPB	chr3:140947369-140947717	MCF-7	breast:	n/a	n/a
18	RAD21	chr3:140947147-140947586	MCF-7	breast:	n/a	n/a
19	RAD21	chr3:140947301-140947525	HepG2	liver:	n/a	n/a
20	CTCF	chr3:140947118-140947573	MCF-7	breast:	n/a	n/a
21	MAX	chr3:140947208-140947688	MCF-7	breast:	n/a	n/a
22	FOXA2	chr3:140947265-140947717	A549	lung:	n/a	n/a
23	FOXA1	chr3:140947202-140947774	T-47D	breast:	n/a	chr3:140947500-140947515
24	TCF12	chr3:140947129-140947733	A549	lung:	n/a	n/a

Variant related genes	Relation type
ACPL2	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16851185	1.00[MEX][hapmap]
rs16851204	0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16851210	1.00[CEU][hapmap]
rs16851254	0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3796260	0.86[JPT][hapmap]
rs6779202	1.00[CEU][hapmap]
rs7643005	1.00[CEU][hapmap]

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	nsv460870	chr3:140938546-141005574	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv591892	chr3:140938546-141005574	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140940000-140949400	Weak transcription	Fetal Heart	heart
2	chr3:140945200-140947600	Enhancers	Dnd41	blood
3	chr3:140945600-140948000	Enhancers	Fetal Intestine Large	intestine
4	chr3:140945600-140949800	Enhancers	Fetal Stomach	stomach
5	chr3:140945600-140950000	Enhancers	Fetal Lung	lung
6	chr3:140945800-140949600	Enhancers	Fetal Thymus	thymus
7	chr3:140946000-140947600	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:140946000-140948000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:140946000-140948200	Enhancers	Brain Germinal Matrix	brain
10	chr3:140946000-140949800	Enhancers	Fetal Intestine Small	intestine
11	chr3:140946000-140950000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:140946000-140950000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:140946200-140947800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:140946200-140948200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:140946400-140947800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:140946400-140947800	Weak transcription	Fetal Kidney	kidney
17	chr3:140946600-140947600	Enhancers	A549	lung
18	chr3:140946600-140948000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:140946600-140948600	Enhancers	HepG2	liver
20	chr3:140946600-140949400	Weak transcription	NH-A	brain
21	chr3:140946800-140949600	Enhancers	Thymus	Thymus
22	chr3:140947000-140949400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:140947000-140949400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:140947000-140949600	Weak transcription	HSMM	muscle
25	chr3:140947000-140949600	Weak transcription	HSMMtube	muscle
26	chr3:140947000-140949800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:140947200-140947600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:140947200-140947600	Weak transcription	Fetal Brain Female	brain
29	chr3:140947200-140949600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:140947200-140949800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:140947400-140947600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr3:140947400-140949400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:140947400-140949400	Weak transcription	Duodenum Mucosa	Duodenum

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