Variant report

Variant	rs10260230
Chromosome Location	chr7:40172997-40172998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:40168616-40174782	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr7:40172722-40173193	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:40171616-40174820	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr7:40168497-40173052	K562	blood:	n/a	n/a
5	E2F4	chr7:40172911-40173117	MCF10A-Er-Src	breast:	n/a	n/a
6	MXI1	chr7:40171702-40175255	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr7:40172945-40174952	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:40167264..40171884-chr7:40172209..40175327,5	K562	blood:
2	chr7:40167562..40171134-chr7:40171634..40175290,4	MCF-7	breast:
3	chr7:39989838..39991458-chr7:40172726..40174247,2	K562	blood:
4	chr20:45945819..45948556-chr7:40171300..40173134,2	MCF-7	breast:
5	chr7:39957754..39959391-chr7:40170682..40173574,2	MCF-7	breast:
6	chr7:39985235..39991458-chr7:40172332..40176244,8	K562	blood:
7	chr7:40165267..40167211-chr7:40171970..40173571,2	K562	blood:
8	chr7:40162725..40164570-chr7:40170579..40173215,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf10-4	chr7:40172588-40174207	NONHSAT120246

No data

Variant related genes	Relation type
SUGCT	TF binding region
ENSG00000101040	Chromatin interaction
ENSG00000199273	Chromatin interaction
ENSG00000065883	Chromatin interaction
ENSG00000259826	Chromatin interaction
ENSG00000267882	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10232126	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10236765	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10243820	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10244698	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10256299	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10256385	0.87[AFR][1000 genomes]
rs10261306	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263620	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263812	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10265714	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10282322	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1529067	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17171660	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17171663	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28465563	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28491242	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28548682	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55731554	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6956047	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73687514	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7784684	1.00[EUR][1000 genomes]
rs7793901	1.00[EUR][1000 genomes]
rs7807456	1.00[EUR][1000 genomes]
rs7808779	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1024735	chr7:40149227-40203356	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40134600-40173200	Weak transcription	Lung	lung
2	chr7:40135600-40173000	Weak transcription	Fetal Muscle Leg	muscle
3	chr7:40136600-40173200	Weak transcription	Placenta	Placenta
4	chr7:40163000-40173200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:40165800-40173400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:40167800-40173000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:40167800-40173000	Weak transcription	Fetal Thymus	thymus
8	chr7:40167800-40173200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr7:40169200-40173200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:40169200-40173200	Weak transcription	Pancreas	Pancrea
11	chr7:40169400-40173200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:40170000-40173000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:40170400-40173200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr7:40171000-40173000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr7:40171400-40173200	Enhancers	Brain Substantia Nigra	brain
16	chr7:40171400-40173200	Weak transcription	Esophagus	oesophagus
17	chr7:40171400-40173600	Weak transcription	Spleen	Spleen
18	chr7:40171600-40173200	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr7:40171600-40173200	Weak transcription	Left Ventricle	heart
20	chr7:40171600-40173600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:40171600-40173600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:40171800-40173000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr7:40171800-40173000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr7:40171800-40173000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:40171800-40173000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:40171800-40173200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr7:40171800-40173200	Enhancers	Brain Cingulate Gyrus	brain
28	chr7:40171800-40173200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr7:40172000-40173000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:40172000-40173000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr7:40172000-40173200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr7:40172000-40175000	Active TSS	K562	blood
33	chr7:40172200-40173000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:40172200-40173000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr7:40172200-40173400	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr7:40172200-40173400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr7:40172200-40173400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:40172200-40173400	Flanking Active TSS	Dnd41	blood
39	chr7:40172200-40174600	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr7:40172200-40175200	Active TSS	HMEC	breast
41	chr7:40172400-40173000	Flanking Active TSS	NHDF-Ad	bronchial
42	chr7:40172400-40173200	Enhancers	Primary B cells from peripheral blood	blood
43	chr7:40172400-40173200	Enhancers	Fetal Brain Male	brain
44	chr7:40172400-40173200	Enhancers	Thymus	Thymus
45	chr7:40172400-40173200	Flanking Active TSS	A549	lung
46	chr7:40172400-40173400	Flanking Active TSS	Osteobl	bone
47	chr7:40172400-40173600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:40172400-40174800	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr7:40172400-40175000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr7:40172400-40175200	Active TSS	HSMMtube	muscle

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