Variant report

Variant	rs12071299
Chromosome Location	chr1:246843489-246843490
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	GATA2	chr1:246843231-246844204	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246842065..246844479-chr1:246852979..246855083,3	K562	blood:

Variant related genes	Relation type
ENSG00000260698	TF binding region
ENSG00000235021	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10732299	1.00[AMR][1000 genomes]
rs10924822	1.00[AMR][1000 genomes]
rs12040914	1.00[AMR][1000 genomes]
rs12069175	1.00[AMR][1000 genomes]
rs2996552	1.00[AMR][1000 genomes]
rs3007320	1.00[AMR][1000 genomes]
rs3007321	1.00[AMR][1000 genomes]
rs3007325	1.00[AMR][1000 genomes]
rs3007326	1.00[AMR][1000 genomes]
rs3007327	1.00[AMR][1000 genomes]
rs4244625	1.00[AMR][1000 genomes]
rs4244626	1.00[AMR][1000 genomes]
rs4244629	1.00[AMR][1000 genomes]
rs4511163	1.00[AMR][1000 genomes]
rs4532864	1.00[AMR][1000 genomes]
rs4926452	1.00[AMR][1000 genomes]
rs4926463	1.00[AMR][1000 genomes]
rs6426335	1.00[AMR][1000 genomes]
rs6663093	1.00[AMR][1000 genomes]
rs6696798	1.00[AMR][1000 genomes]
rs7416659	1.00[AMR][1000 genomes]
rs9426266	1.00[AMR][1000 genomes]
rs9426274	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv1002595	chr1:246774036-246846548	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1007194	chr1:246813090-246855424	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246822200-246845200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:246829400-246844000	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:246829600-246845200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:246829800-246844400	Weak transcription	Spleen	Spleen
5	chr1:246829800-246845200	Weak transcription	Fetal Lung	lung
6	chr1:246829800-246845200	Weak transcription	Ovary	ovary
7	chr1:246829800-246853000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:246830200-246853000	Weak transcription	Fetal Brain Female	brain
9	chr1:246832400-246844000	Weak transcription	Right Ventricle	heart
10	chr1:246832400-246853000	Weak transcription	Thymus	Thymus
11	chr1:246832400-246856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:246832600-246845000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:246833400-246845200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:246833600-246843600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:246833800-246845200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:246833800-246850000	Weak transcription	Primary T cells from cord blood	blood
17	chr1:246834000-246844400	Weak transcription	Adipose Nuclei	Adipose
18	chr1:246834000-246845000	Weak transcription	Osteobl	bone
19	chr1:246834600-246845000	Weak transcription	Primary B cells from cord blood	blood
20	chr1:246840000-246844800	Enhancers	Fetal Intestine Large	intestine
21	chr1:246840000-246845400	Enhancers	Fetal Intestine Small	intestine
22	chr1:246840800-246845200	Weak transcription	Colonic Mucosa	Colon
23	chr1:246841200-246844000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:246841400-246845200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:246841400-246845200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:246841400-246845400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:246842200-246843600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:246842200-246847000	Enhancers	Fetal Muscle Leg	muscle
29	chr1:246842400-246844000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr1:246842400-246844000	Enhancers	Duodenum Mucosa	Duodenum
31	chr1:246842400-246845800	Enhancers	NHLF	lung
32	chr1:246842400-246846400	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:246842400-246846400	Enhancers	Fetal Stomach	stomach
34	chr1:246842400-246850800	Enhancers	Placenta	Placenta
35	chr1:246842600-246843600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:246842600-246843800	Enhancers	HSMMtube	muscle
37	chr1:246842600-246844600	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:246842600-246844800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr1:246842800-246843600	Enhancers	HSMM	muscle
40	chr1:246842800-246843800	Enhancers	Brain Angular Gyrus	brain
41	chr1:246842800-246844200	Enhancers	Left Ventricle	heart
42	chr1:246842800-246844400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:246842800-246845000	Enhancers	Fetal Kidney	kidney
44	chr1:246842800-246845400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:246842800-246845400	Enhancers	Psoas Muscle	Psoas
46	chr1:246843000-246843800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:246843000-246843800	Enhancers	Brain Anterior Caudate	brain
48	chr1:246843000-246844000	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:246843000-246844000	Enhancers	Brain Hippocampus Middle	brain
50	chr1:246843000-246844400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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