Variant report

Variant	rs1982642
Chromosome Location	chr3:140946961-140946962
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	chr3:140946492-140947554	SH-SY5Y	brain:	n/a	n/a
2	EP300	chr3:140945422-140948945	SK-N-SH	brain:	n/a	chr3:140945945-140945959 chr3:140946516-140946530
3	TCF12	chr3:140946381-140947172	SK-N-SH	brain:	n/a	chr3:140947004-140947011
4	TCF12	chr3:140946459-140947168	SK-N-SH	brain:	n/a	chr3:140947004-140947011
5	RAD21	chr3:140946557-140946965	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr3:140946500-140947047	SK-N-SH_RA	brain:	n/a	chr3:140946516-140946530
7	GATA2	chr3:140946595-140947132	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr3:140946461-140947238	SK-N-SH	brain:	n/a	n/a
9	CEBPB	chr3:140946598-140946975	IMR90	lung:	n/a	n/a
10	YY1	chr3:140946522-140947047	SK-N-SH_RA	brain:	n/a	n/a
11	GATA3	chr3:140946409-140947090	SK-N-SH	brain:	n/a	n/a
12	EP300	chr3:140946524-140947055	SK-N-SH_RA	brain:	n/a	n/a
13	POLR2A	chr3:140946523-140947000	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140945385..140947466-chr3:140997029..140999166,2	MCF-7	breast:
2	chr3:140945648..140947286-chr3:140948791..140951390,2	K562	blood:

Variant related genes	Relation type
ACPL2	TF binding region
ENSG00000155893	Chromatin interaction

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

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

rs_ID	r²[population]
rs10935421	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12053839	0.94[AMR][1000 genomes]
rs12486678	1.00[AMR][1000 genomes]
rs12495839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12497626	1.00[AFR][1000 genomes]
rs12633778	0.94[AMR][1000 genomes]
rs16851167	0.94[AMR][1000 genomes];0.98[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	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:35 , 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	chr3:140946000-140947000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:140946000-140947600	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:140946000-140948000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:140946000-140948200	Enhancers	Brain Germinal Matrix	brain
11	chr3:140946000-140949800	Enhancers	Fetal Intestine Small	intestine
12	chr3:140946000-140950000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:140946000-140950000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:140946200-140947000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:140946200-140947200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:140946200-140947400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:140946200-140947400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:140946200-140947800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:140946200-140948200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:140946400-140947000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:140946400-140947000	Enhancers	HSMM	muscle
22	chr3:140946400-140947200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr3:140946400-140947800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:140946400-140947800	Weak transcription	Fetal Kidney	kidney
25	chr3:140946600-140947200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:140946600-140947600	Enhancers	A549	lung
27	chr3:140946600-140948000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:140946600-140948600	Enhancers	HepG2	liver
29	chr3:140946600-140949400	Weak transcription	NH-A	brain
30	chr3:140946800-140947000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:140946800-140947000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:140946800-140947000	Enhancers	HSMMtube	muscle
33	chr3:140946800-140947200	Enhancers	Fetal Brain Female	brain
34	chr3:140946800-140947400	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:140946800-140949600	Enhancers	Thymus	Thymus

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