Variant report

Variant	rs10267405
Chromosome Location	chr7:7594892-7594893
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	SETDB1	chr7:7594419-7595021	U2OS	brain:	n/a	n/a
2	TCF7L2	chr7:7593576-7595058	HEK293	kidney:	n/a	chr7:7594662-7594678 chr7:7594662-7594678
3	KAP1	chr7:7593215-7595132	HEK293	kidney:	n/a	n/a
4	KAP1	chr7:7594437-7595037	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7594653..7598119-chr7:7605065..7607916,4	MCF-7	breast:
2	chr7:7473373..7475762-chr7:7594753..7597282,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL28A1-1	chr7:7594787-7594928	XLOC_006350

Variant related genes	Relation type
ENSG00000272894	TF binding region
ENSG00000272732	TF binding region
ENSG00000272894	Chromatin interaction
ENSG00000164654	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10085615	1.00[AMR][1000 genomes]
rs10085678	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10085695	1.00[MEX][hapmap]
rs10224056	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10226442	1.00[AMR][1000 genomes]
rs10227544	1.00[AMR][1000 genomes]
rs10237888	1.00[AMR][1000 genomes]
rs10242691	1.00[AMR][1000 genomes]
rs10244335	1.00[AMR][1000 genomes]
rs10244366	1.00[AMR][1000 genomes]
rs10244757	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10246309	1.00[AMR][1000 genomes]
rs10247226	1.00[AMR][1000 genomes]
rs10249422	1.00[MEX][hapmap]
rs10255581	1.00[AMR][1000 genomes]
rs10257117	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10257279	1.00[AMR][1000 genomes]
rs10257458	1.00[AMR][1000 genomes]
rs10258922	1.00[AMR][1000 genomes]
rs10259911	1.00[AMR][1000 genomes]
rs10262309	1.00[AMR][1000 genomes]
rs10265415	1.00[YRI][hapmap]
rs10266393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10269709	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10275145	1.00[MEX][hapmap]
rs10278024	1.00[AMR][1000 genomes]
rs10280185	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap]
rs10280723	1.00[MEX][hapmap]
rs10282183	1.00[AMR][1000 genomes]
rs12333875	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs12334276	1.00[AMR][1000 genomes]
rs13438746	1.00[MEX][hapmap]
rs17168530	1.00[AMR][1000 genomes]
rs17169196	1.00[MEX][hapmap]
rs28442228	1.00[AMR][1000 genomes]
rs28535494	1.00[AMR][1000 genomes]
rs28565038	1.00[AMR][1000 genomes]
rs28602992	1.00[AMR][1000 genomes]
rs28681690	1.00[AMR][1000 genomes]
rs28712138	1.00[AMR][1000 genomes]
rs28842558	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6951703	1.00[AMR][1000 genomes]
rs7778417	1.00[AMR][1000 genomes]
rs7791164	1.00[AMR][1000 genomes]
rs7805479	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs7810456	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv887473	chr7:7497676-7604913	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1027872	chr7:7516124-7600842	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1024107	chr7:7516124-7601638	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv887474	chr7:7519603-7679644	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
12	nsv887475	chr7:7519603-7679644	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv887476	chr7:7519603-7680697	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
15	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
16	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7581800-7595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:7589400-7605800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr7:7589800-7596000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:7589800-7596000	Weak transcription	Aorta	Aorta
5	chr7:7589800-7596000	Weak transcription	Placenta	Placenta
6	chr7:7589800-7596600	Weak transcription	Gastric	stomach
7	chr7:7590000-7595000	Weak transcription	Brain Hippocampus Middle	brain
8	chr7:7590000-7606000	Weak transcription	Brain Substantia Nigra	brain
9	chr7:7590000-7606200	Weak transcription	Ovary	ovary
10	chr7:7590200-7605800	Weak transcription	Brain Anterior Caudate	brain
11	chr7:7590200-7605800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr7:7592000-7596400	Weak transcription	Lung	lung
13	chr7:7592400-7599200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:7593600-7595200	Enhancers	Fetal Muscle Leg	muscle
15	chr7:7593600-7595200	Enhancers	Pancreas	Pancrea
16	chr7:7593800-7595000	Enhancers	Liver	Liver
17	chr7:7593800-7595200	Enhancers	Osteobl	bone
18	chr7:7593800-7595400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr7:7593800-7595400	Enhancers	NHDF-Ad	bronchial
20	chr7:7593800-7606000	Weak transcription	Right Atrium	heart
21	chr7:7594000-7595200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr7:7594000-7595200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr7:7594200-7595200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr7:7594400-7595000	Active TSS	Psoas Muscle	Psoas
25	chr7:7594400-7597000	Enhancers	Brain Germinal Matrix	brain
26	chr7:7594600-7595000	Flanking Active TSS	HSMM	muscle
27	chr7:7594600-7595000	Flanking Active TSS	HSMMtube	muscle
28	chr7:7594600-7595200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:7594600-7595400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:7594800-7595200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr7:7594800-7595200	Enhancers	Skeletal Muscle Female	skeletal muscle

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