Variant report

Variant	rs7790080
Chromosome Location	chr7:107031322-107031323
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	chr7:107028832..107031343-chr7:107040256..107041965,2	K562	blood:
2	chr7:107028942..107031560-chr7:107035315..107037970,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1015411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10224503	0.83[AMR][1000 genomes]
rs10234355	1.00[CHB][hapmap]
rs10264412	0.86[AMR][1000 genomes]
rs10267907	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10276604	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10281535	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11535285	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs11977187	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs12112877	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12667527	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12672451	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs12673675	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs13230144	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17153981	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17154040	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17154091	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1858888	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2023685	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2057837	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2066735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2107317	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2237661	0.95[CEU][hapmap]
rs2237665	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2237668	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237671	0.86[AMR][1000 genomes]
rs2237677	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2237678	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2253146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253269	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253271	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2253833	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283038	0.90[CEU][hapmap]
rs2395868	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2395869	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395882	0.80[ASN][1000 genomes]
rs2520241	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2520242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2520243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2520245	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2520249	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2520250	0.87[AMR][1000 genomes]
rs2520256	0.87[AMR][1000 genomes]
rs2520268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2520269	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2712195	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs2712196	0.86[AMR][1000 genomes]
rs2712201	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2712224	0.84[AMR][1000 genomes]
rs3094383	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34325395	0.87[AMR][1000 genomes]
rs3801964	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4727678	0.90[AMR][1000 genomes]
rs4727679	0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4727680	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4727681	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4727684	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4730235	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730237	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4730238	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730245	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs58391518	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62482493	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62482495	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62482499	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62482502	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62482503	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62482507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62482543	0.81[ASN][1000 genomes]
rs62483633	0.86[EUR][1000 genomes]
rs62483634	0.86[EUR][1000 genomes]
rs62483640	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62483641	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62483725	0.82[AMR][1000 genomes]
rs6949634	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6976607	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7777950	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7778250	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7778270	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7785892	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7786801	0.80[ASN][1000 genomes]
rs7788271	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7788330	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7803151	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9791733	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs982447	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs986994	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv608073	chr7:106960515-107063686	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7790080	BCAP29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107001400-107037600	Weak transcription	Spleen	Spleen
2	chr7:107001400-107053600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:107003200-107031400	Weak transcription	Fetal Intestine Large	intestine
4	chr7:107003600-107045000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:107003800-107038800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr7:107003800-107048400	Weak transcription	Dnd41	blood
7	chr7:107003800-107050200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr7:107008400-107048200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:107013200-107038600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr7:107022200-107053000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:107024600-107038200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr7:107024600-107045000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:107025000-107038800	Weak transcription	Lung	lung
14	chr7:107025000-107039800	Weak transcription	Fetal Intestine Small	intestine
15	chr7:107025800-107039600	Weak transcription	Primary T cells from cord blood	blood
16	chr7:107027400-107035000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:107027400-107045800	Weak transcription	Right Atrium	heart
18	chr7:107027400-107053400	Weak transcription	Gastric	stomach
19	chr7:107027800-107047200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr7:107027800-107050200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:107027800-107086800	Weak transcription	Aorta	Aorta
22	chr7:107028000-107031400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:107028000-107038800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:107028000-107038800	Weak transcription	Psoas Muscle	Psoas
25	chr7:107028000-107044800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:107028000-107052800	Weak transcription	Fetal Muscle Leg	muscle
27	chr7:107028000-107054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:107028200-107031400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:107028200-107039800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr7:107028200-107053000	Weak transcription	Fetal Stomach	stomach
31	chr7:107028200-107082400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:107028200-107103800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:107028600-107033200	Weak transcription	Adipose Nuclei	Adipose
34	chr7:107028800-107032600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:107028800-107033400	Weak transcription	NHDF-Ad	bronchial
36	chr7:107028800-107033600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr7:107028800-107035800	Weak transcription	HUVEC	blood vessel
38	chr7:107028800-107053000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr7:107028800-107053200	Weak transcription	K562	blood
40	chr7:107029000-107033000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:107029000-107033200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:107029000-107034800	Weak transcription	Osteobl	bone
43	chr7:107029000-107035600	Weak transcription	NHLF	lung
44	chr7:107029400-107039800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:107029400-107050400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:107030200-107049000	Weak transcription	Right Ventricle	heart
47	chr7:107030400-107031600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr7:107030600-107031800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:107030600-107031800	Enhancers	Fetal Heart	heart
50	chr7:107030800-107031600	Enhancers	Fetal Kidney	kidney

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