Variant report

Variant	rs62479858
Chromosome Location	chr7:97924226-97924227
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:97922258..97924610-chr7:97924998..97927065,2	K562	blood:
2	chr7:97917308..97920169-chr7:97921716..97924764,3	MCF-7	breast:
3	chr7:97923208..97926071-chr7:98023782..98025314,2	K562	blood:
4	chr7:97922244..97926850-chr7:97930553..97934195,4	MCF-7	breast:
5	chr7:97923913..97924733-chr7:98030300..98031119,2	MCF-7	breast:
6	chr7:97915929..97917893-chr7:97922819..97924333,2	MCF-7	breast:
7	chr7:97918116..97920073-chr7:97921586..97924329,2	MCF-7	breast:
8	chr7:97910688..97912984-chr7:97923702..97926466,2	MCF-7	breast:
9	chr7:97924151..97925228-chr7:98050010..98050830,5	MCF-7	breast:
10	chr7:97921091..97922679-chr7:97923394..97926029,2	MCF-7	breast:
11	chr7:97923862..97924526-chr7:98434595..98435120,2	K562	blood:
12	chr7:97913545..97915721-chr7:97921794..97924476,3	MCF-7	breast:
13	chr7:97922243..97926579-chr7:98028416..98031762,5	MCF-7	breast:
14	chr7:97923819..97924747-chr7:98030158..98031061,6	K562	blood:
15	chr7:97922907..97924787-chr7:97933166..97935079,2	K562	blood:
16	chr7:97923822..97924821-chr7:98030187..98031111,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000006453	Chromatin interaction
ENSG00000164713	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1006169	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10953254	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11768214	0.89[ASN][1000 genomes]
rs11768599	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11769950	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772432	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12533982	0.83[AMR][1000 genomes]
rs12536125	0.87[ASN][1000 genomes]
rs12539761	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1541409	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17169486	0.87[ASN][1000 genomes]
rs1985593	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240348	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3801258	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3944111	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4236537	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4729432	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55648546	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55946416	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56997921	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59120980	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62478160	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62478201	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62478228	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62478235	0.84[AMR][1000 genomes]
rs62479844	0.90[ASN][1000 genomes]
rs9640655	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9641236	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9641237	0.81[ASN][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	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1033029	chr7:97773232-98017992	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv539033	chr7:97773232-98017992	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv888760	chr7:97816327-97965016	Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv831067	chr7:97860169-98065528	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1026477	chr7:97869446-98034129	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	esv1802449	chr7:97900191-97929668	Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62479858	BAIAP2L1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97914200-97925400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:97914200-97958400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:97914800-97924600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:97916000-97927000	Weak transcription	Fetal Brain Male	brain
5	chr7:97916200-97930400	Weak transcription	K562	blood
6	chr7:97916200-97933800	Strong transcription	Fetal Stomach	stomach
7	chr7:97916600-97924400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:97917200-97925400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:97917200-97926800	Strong transcription	Osteobl	bone
10	chr7:97917600-97924400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:97917800-97924400	Strong transcription	Fetal Intestine Large	intestine
12	chr7:97917800-97924600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr7:97917800-97924800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:97917800-97925600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:97917800-97926400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr7:97917800-97926800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:97918000-97927200	Strong transcription	NHLF	lung
18	chr7:97919000-97924400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:97919000-97924400	Strong transcription	Ovary	ovary
20	chr7:97919000-97926600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr7:97919000-97926800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:97919000-97941200	Weak transcription	Psoas Muscle	Psoas
23	chr7:97919200-97957600	Weak transcription	Right Atrium	heart
24	chr7:97919400-97924400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr7:97919400-97926200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr7:97919400-97926600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr7:97919800-97926800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr7:97920000-97927000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr7:97920200-97925400	Strong transcription	Primary T cells from cord blood	blood
30	chr7:97920200-97925600	Strong transcription	Brain Germinal Matrix	brain
31	chr7:97920200-97926400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr7:97920400-97925400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:97920400-97925400	Strong transcription	Hela-S3	cervix
34	chr7:97920400-97927600	Strong transcription	Colonic Mucosa	Colon
35	chr7:97920600-97924400	Strong transcription	Lung	lung
36	chr7:97920600-97925400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:97920800-97925000	Strong transcription	Rectal Smooth Muscle	rectum
38	chr7:97922000-97924400	Weak transcription	Fetal Thymus	thymus
39	chr7:97922200-97924400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:97922200-97924400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:97922200-97924600	Weak transcription	Brain Angular Gyrus	brain
42	chr7:97922200-97926800	Weak transcription	Thymus	Thymus
43	chr7:97922200-97935200	Weak transcription	Fetal Heart	heart
44	chr7:97922200-97946800	Weak transcription	Small Intestine	intestine
45	chr7:97922600-97924400	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:97922600-97931400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:97922800-97927600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr7:97922800-97935400	Weak transcription	Fetal Lung	lung
49	chr7:97923000-97924400	Weak transcription	Brain Substantia Nigra	brain
50	chr7:97923000-97925000	Genic enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links