Variant report

Variant	rs1146042
Chromosome Location	chr7:40124137-40124138
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:40115479..40117853-chr7:40121950..40124630,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1267263	0.85[EUR][1000 genomes]
rs17171657	0.88[CHD][hapmap]
rs17496102	0.86[ASN][1000 genomes]
rs1798988	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2329694	1.00[CEU][hapmap]
rs3930486	1.00[JPT][hapmap]
rs6950489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs695078	0.85[EUR][1000 genomes]
rs6966734	1.00[CEU][hapmap]
rs699513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs773407	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs798852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs798857	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs798863	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
2	nsv1015322	chr7:40006195-40141195	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv2761319	chr7:40006195-40142139	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv464436	chr7:40018693-40133044	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv606706	chr7:40018693-40133044	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv606707	chr7:40021044-40133044	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv606708	chr7:40021044-40157040	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	nsv887978	chr7:40030488-40124137	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv429748	chr7:40054760-40140660	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	esv2756801	chr7:40060180-40269583	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	esv2759525	chr7:40060180-40269583	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv887979	chr7:40067021-40193535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv887980	chr7:40067021-40203356	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv887981	chr7:40075461-40203356	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv971193	chr7:40075881-40197955	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	esv34547	chr7:40077032-40230965	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv824080	chr7:40077089-40198644	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	nsv464437	chr7:40094641-40197168	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
19	nsv606709	chr7:40094641-40197168	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
20	nsv1032278	chr7:40097371-40396300	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
21	nsv887982	chr7:40098787-40193535	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40028000-40127800	Weak transcription	Colonic Mucosa	Colon
2	chr7:40043600-40127800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:40055600-40126400	Weak transcription	Aorta	Aorta
4	chr7:40055800-40127600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:40055800-40127600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:40056200-40128600	Weak transcription	A549	lung
7	chr7:40058600-40126800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:40059000-40125200	Weak transcription	Fetal Kidney	kidney
9	chr7:40072000-40130400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:40077200-40127800	Weak transcription	Esophagus	oesophagus
11	chr7:40080200-40132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:40082000-40127800	Weak transcription	Pancreas	Pancrea
13	chr7:40082600-40128200	Weak transcription	Spleen	Spleen
14	chr7:40083400-40127400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr7:40086400-40127800	Weak transcription	Thymus	Thymus
16	chr7:40092600-40127600	Weak transcription	Brain Substantia Nigra	brain
17	chr7:40093800-40127600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:40094800-40127800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:40095800-40127800	Weak transcription	Fetal Brain Female	brain
20	chr7:40096600-40126600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:40096800-40126600	Weak transcription	Lung	lung
22	chr7:40097200-40127600	Weak transcription	HSMMtube	muscle
23	chr7:40097200-40132600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:40097200-40132600	Weak transcription	Right Ventricle	heart
25	chr7:40098200-40132400	Weak transcription	Psoas Muscle	Psoas
26	chr7:40098600-40127600	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:40099000-40126600	Weak transcription	Brain Angular Gyrus	brain
28	chr7:40099800-40132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:40103000-40126200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr7:40103000-40126400	Weak transcription	HUVEC	blood vessel
31	chr7:40103000-40127600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr7:40103000-40127600	Weak transcription	NHEK	skin
33	chr7:40103000-40131400	Weak transcription	NHLF	lung
34	chr7:40103200-40126800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:40103600-40126600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:40104000-40126600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:40104400-40127600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr7:40105600-40126600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr7:40106000-40127600	Weak transcription	Hela-S3	cervix
40	chr7:40106000-40127800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:40106000-40131400	Weak transcription	HMEC	breast
42	chr7:40106800-40127800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:40107000-40127800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr7:40108000-40124200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr7:40108800-40126600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:40109200-40124400	Weak transcription	Primary T cells from cord blood	blood
47	chr7:40109600-40126600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr7:40111600-40124400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr7:40112600-40127800	Weak transcription	HepG2	liver
50	chr7:40116000-40127400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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