Variant report

Variant	rs2240384
Chromosome Location	chr7:99027044-99027045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99021211..99022744-chr7:99025529..99028020,2	MCF-7	breast:
2	chr7:99005571..99007892-chr7:99025987..99028381,2	MCF-7	breast:
3	chr7:99026847..99029073-chr7:99029475..99031383,3	K562	blood:
4	chr7:99015297..99018039-chr7:99026570..99029303,2	K562	blood:
5	chr7:99026500..99029422-chr7:99032400..99035110,2	K562	blood:
6	chr7:99019766..99021951-chr7:99025804..99027414,2	MCF-7	breast:
7	chr7:99025112..99027290-chr7:99035346..99038143,2	K562	blood:
8	chr7:99025099..99027768-chr7:99034111..99036844,3	MCF-7	breast:
9	chr7:99020429..99023882-chr7:99024975..99028179,3	K562	blood:
10	chr7:99004290..99006114-chr7:99025633..99027496,2	K562	blood:
11	chr7:99020471..99023882-chr7:99024975..99028185,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000106244	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1011024	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10155966	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10225314	0.87[JPT][hapmap]
rs10238965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10243678	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10244158	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10253937	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10254729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap]
rs10270459	0.92[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs10270917	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs10271049	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271582	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10272998	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap]
rs10279308	0.84[CEU][hapmap]
rs1043466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10464604	0.86[ASN][1000 genomes]
rs11539770	0.86[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs11772470	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs11976018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11978089	0.84[CEU][hapmap]
rs12538826	0.87[ASN][1000 genomes]
rs13227795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13240600	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13437771	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980307	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];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2003499	0.84[CEU][hapmap]
rs2072181	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2240385	0.86[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2272168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280600	0.91[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];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286162	0.92[CEU][hapmap]
rs2404324	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs28457808	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28495024	0.81[AMR][1000 genomes]
rs3137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34777615	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3779354	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3800960	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap]
rs3801288	0.92[CEU][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs3843540	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3901286	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs45492098	0.82[ASN][1000 genomes]
rs45540134	0.82[ASN][1000 genomes]
rs45622743	0.84[ASN][1000 genomes]
rs4729532	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs61159815	0.81[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap]
rs6955490	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs6961634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6962772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794682	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804551	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs868564	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs883403	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs940336	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2240384	CPSF4	cis	parietal	SCAN
rs2240384	CYP3A5	cis	parietal	SCAN
rs2240384	ACTL6B	cis	cerebellum	SCAN
rs2240384	GATS	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99011400-99035000	Weak transcription	Fetal Brain Male	brain
3	chr7:99011600-99032200	Weak transcription	NHDF-Ad	bronchial
4	chr7:99013200-99028800	Strong transcription	Fetal Intestine Small	intestine
5	chr7:99015600-99035200	Weak transcription	Fetal Kidney	kidney
6	chr7:99015600-99035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr7:99015600-99035600	Weak transcription	Stomach Mucosa	stomach
8	chr7:99016800-99036000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:99017600-99030200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:99017600-99035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr7:99018200-99035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:99018200-99035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr7:99018400-99035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:99020200-99030000	Weak transcription	HSMM	muscle
15	chr7:99021400-99034400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:99021600-99035200	Weak transcription	HMEC	breast
17	chr7:99022200-99035400	Weak transcription	NH-A	brain
18	chr7:99023000-99027800	Weak transcription	Osteobl	bone
19	chr7:99023000-99036000	Weak transcription	Small Intestine	intestine
20	chr7:99025600-99028400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:99025600-99028600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr7:99025600-99028600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:99025600-99028600	Strong transcription	Brain Substantia Nigra	brain
24	chr7:99025600-99031400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr7:99025600-99033000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:99025600-99033000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr7:99025600-99033000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr7:99025600-99033000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:99025600-99033200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:99025600-99033200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:99025600-99033400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr7:99025600-99033400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:99025600-99033800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:99025600-99034400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr7:99025600-99034800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:99025600-99034800	Strong transcription	Fetal Muscle Leg	muscle
37	chr7:99025600-99035200	Strong transcription	Fetal Stomach	stomach
38	chr7:99025800-99028200	Strong transcription	NHEK	skin
39	chr7:99025800-99031200	Strong transcription	Thymus	Thymus
40	chr7:99025800-99033000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:99025800-99033200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr7:99025800-99034000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:99026000-99028200	Strong transcription	Fetal Lung	lung
44	chr7:99026000-99028400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:99026000-99032800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr7:99026000-99032800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:99026000-99033200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr7:99026200-99028200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:99026200-99028400	Strong transcription	Colon Smooth Muscle	Colon
50	chr7:99026200-99028400	Strong transcription	Fetal Intestine Large	intestine

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