Variant report

Variant	rs3007309
Chromosome Location	chr1:246866803-246866804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:246866592..246869199-chr1:246886692..246890218,3	MCF-7	breast:
2	chr1:246862143..246864092-chr1:246865510..246867790,2	MCF-7	breast:
3	chr1:246862708..246864361-chr1:246864817..246867078,2	K562	blood:
4	chr1:246866395..246870620-chr1:246886545..246889011,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143653	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12725791	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3007307	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3007308	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007310	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007311	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007312	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007313	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6426323	0.86[EUR][1000 genomes]
rs7520737	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532929	0.86[EUR][1000 genomes]
rs9426213	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
9	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246860200-246867400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:246862600-246867000	Weak transcription	Thymus	Thymus
3	chr1:246862600-246872800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:246862800-246867000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:246862800-246868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:246862800-246868200	Weak transcription	HMEC	breast
7	chr1:246862800-246871000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:246863000-246867000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:246863000-246867000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:246863000-246867000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:246863000-246867000	Weak transcription	Placenta	Placenta
12	chr1:246863000-246867000	Weak transcription	NHLF	lung
13	chr1:246863000-246867200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:246863000-246867200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:246863000-246868200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:246863000-246868400	Weak transcription	HSMMtube	muscle
17	chr1:246863000-246868400	Weak transcription	NH-A	brain
18	chr1:246863000-246869000	Weak transcription	Fetal Intestine Large	intestine
19	chr1:246863000-246871000	Weak transcription	Primary B cells from cord blood	blood
20	chr1:246864000-246867800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:246864200-246867200	Weak transcription	NHDF-Ad	bronchial
22	chr1:246865200-246867600	Weak transcription	HSMM	muscle
23	chr1:246866000-246867000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:246866400-246868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:246866600-246867800	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:246866600-246867800	Enhancers	Dnd41	blood
27	chr1:246866600-246874000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:246866800-246867200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:246866800-246867400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr1:246866800-246867400	Enhancers	Spleen	Spleen
31	chr1:246866800-246867600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:246866800-246867600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr1:246866800-246868000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr1:246866800-246868000	Enhancers	Stomach Mucosa	stomach

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