Variant report

Variant	rs3109116
Chromosome Location	chr7:112075830-112075831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:
2	chr7:112070004..112076448-chr7:112089182..112092278,11	K562	blood:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10046468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10224789	0.93[ASN][1000 genomes]
rs10227494	1.00[ASN][1000 genomes]
rs10232109	1.00[ASN][1000 genomes]
rs10232110	1.00[ASN][1000 genomes]
rs10237213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10239663	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10243005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10246422	1.00[ASN][1000 genomes]
rs10248314	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10251698	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10253148	0.86[ASN][1000 genomes]
rs10261860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10266976	1.00[ASN][1000 genomes]
rs10269057	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10274016	0.93[ASN][1000 genomes]
rs10275406	1.00[ASN][1000 genomes]
rs10276140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10276369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10276727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10276853	1.00[ASN][1000 genomes]
rs10278420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10281805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10282279	1.00[ASN][1000 genomes]
rs1047550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1047551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12530699	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12532522	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12534930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17159353	1.00[ASN][1000 genomes]
rs17159566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17159604	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17159640	0.87[AMR][1000 genomes]
rs17402962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2285732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28532417	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2894646	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109108	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35134215	1.00[ASN][1000 genomes]
rs41281060	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs56132236	1.00[ASN][1000 genomes]
rs56341778	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57214357	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60127009	1.00[ASN][1000 genomes]
rs60691495	1.00[ASN][1000 genomes]
rs61669542	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67064485	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67604537	1.00[ASN][1000 genomes]
rs6947063	1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6950282	1.00[ASN][1000 genomes]
rs6965896	1.00[ASN][1000 genomes]
rs6969176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73193000	1.00[ASN][1000 genomes]
rs73195204	1.00[ASN][1000 genomes]
rs73195211	1.00[ASN][1000 genomes]
rs73195218	1.00[ASN][1000 genomes]
rs73195220	1.00[ASN][1000 genomes]
rs73195223	1.00[ASN][1000 genomes]
rs73195224	1.00[ASN][1000 genomes]
rs73195225	1.00[ASN][1000 genomes]
rs73197338	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73197343	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73197349	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73197363	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73197366	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73197367	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73197376	1.00[ASN][1000 genomes]
rs7786555	1.00[ASN][1000 genomes]
rs7790065	1.00[ASN][1000 genomes]
rs7806811	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7810149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7810734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7812188	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1801262	chr7:112071795-112104179	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112061000-112089800	Weak transcription	Aorta	Aorta
2	chr7:112064200-112088400	Weak transcription	Psoas Muscle	Psoas
3	chr7:112065800-112079800	Weak transcription	Pancreas	Pancrea
4	chr7:112068600-112077200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr7:112071000-112077000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:112073800-112082400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:112074000-112077200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:112074800-112076000	Enhancers	NHEK	skin
9	chr7:112075400-112076600	Enhancers	A549	lung
10	chr7:112075600-112076800	Weak transcription	HMEC	breast
11	chr7:112075600-112077000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:112075600-112077000	Weak transcription	Hela-S3	cervix
13	chr7:112075600-112077000	Weak transcription	HSMMtube	muscle
14	chr7:112075600-112079600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:112075800-112076600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr7:112075800-112076800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:112075800-112076800	Weak transcription	NH-A	brain
18	chr7:112075800-112077000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:112075800-112077000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:112075800-112077000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr7:112075800-112089800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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