Variant report

Variant	rs3820912
Chromosome Location	chr2:33523658-33523659
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	PBX3	chr2:33522946-33523722	SK-N-SH	brain:	n/a	n/a
2	FOSL2	chr2:33523021-33523760	SK-N-SH	brain:	n/a	chr2:33523405-33523413 chr2:33523404-33523414 chr2:33523404-33523414
3	TCF12	chr2:33523003-33523852	SK-N-SH	brain:	n/a	chr2:33523785-33523793
4	PBX3	chr2:33523006-33523701	SK-N-SH	brain:	n/a	n/a
5	JUND	chr2:33522854-33523802	SK-N-SH	brain:	n/a	chr2:33523405-33523413 chr2:33523404-33523414 chr2:33523404-33523414
6	POLR2A	chr2:33522816-33523711	SK-N-SH	brain:	n/a	n/a
7	STAT3	chr2:33523324-33523778	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr2:33522829-33523863	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr2:33522695-33523859	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr2:33522674-33523792	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr2:33522837-33523882	SK-N-SH	brain:	n/a	chr2:33523785-33523793
12	EP300	chr2:33522873-33523841	SK-N-SH	brain:	n/a	chr2:33523357-33523364

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:33521500..33523864-chr2:33524061..33525573,2	K562	blood:
2	chr2:33514241..33517210-chr2:33520355..33523749,3	K562	blood:

Variant related genes	Relation type
LTBP1	TF binding region
ENSG00000049323	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10495788	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11685108	0.89[ASN][1000 genomes]
rs3754830	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3769528	1.00[EUR][1000 genomes]
rs3769529	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3769534	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3769547	1.00[EUR][1000 genomes]
rs56203414	0.81[ASN][1000 genomes]
rs59246149	1.00[EUR][1000 genomes]
rs6708335	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking 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	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1011020	chr2:33508811-33527784	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
2	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:33502600-33537000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:33505000-33526200	Weak transcription	Placenta	Placenta
5	chr2:33507000-33528600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:33517000-33524600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:33517000-33525400	Weak transcription	Right Ventricle	heart
8	chr2:33517000-33526600	Weak transcription	Fetal Stomach	stomach
9	chr2:33517000-33528800	Weak transcription	Psoas Muscle	Psoas
10	chr2:33517000-33529200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:33517000-33529400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:33517000-33529600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:33517200-33525800	Weak transcription	Liver	Liver
14	chr2:33517200-33533000	Weak transcription	Brain Substantia Nigra	brain
15	chr2:33517200-33533200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:33517200-33537400	Weak transcription	Fetal Brain Male	brain
17	chr2:33517200-33545000	Weak transcription	Fetal Kidney	kidney
18	chr2:33517200-33545800	Weak transcription	Fetal Lung	lung
19	chr2:33517200-33546400	Weak transcription	Brain Angular Gyrus	brain
20	chr2:33517600-33532600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:33517600-33532800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:33517800-33543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:33521400-33525400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:33521800-33525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:33522000-33523800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:33522000-33523800	Enhancers	Colon Smooth Muscle	Colon
27	chr2:33522200-33523800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:33522200-33526200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:33522400-33524000	Enhancers	NH-A	brain
30	chr2:33522400-33527200	Weak transcription	Fetal Muscle Leg	muscle
31	chr2:33522600-33523800	Enhancers	Fetal Heart	heart
32	chr2:33522800-33523800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:33522800-33523800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:33522800-33523800	Enhancers	Osteobl	bone
35	chr2:33522800-33524000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:33522800-33524200	Enhancers	HSMMtube	muscle
37	chr2:33522800-33525400	Weak transcription	Left Ventricle	heart
38	chr2:33522800-33526600	Weak transcription	Aorta	Aorta
39	chr2:33523200-33525400	Weak transcription	NHLF	lung
40	chr2:33523200-33529400	Weak transcription	HUVEC	blood vessel
41	chr2:33523400-33523800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:33523400-33524800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:33523400-33527200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:33523400-33528800	Weak transcription	Ovary	ovary
45	chr2:33523400-33532600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:33523400-33545200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:33523600-33524400	Weak transcription	NHDF-Ad	bronchial
48	chr2:33523600-33525000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:33523600-33526200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:33523600-33528800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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