Variant report

Variant	rs57480158
Chromosome Location	chr1:9886636-9886637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9884569..9887155-chr1:10002902..10004455,2	K562	blood:
2	chr1:9852615..9854985-chr1:9884936..9886688,2	MCF-7	breast:
3	chr1:9882501..9887964-chr1:9906388..9911794,10	MCF-7	breast:
4	chr1:9884699..9887504-chr1:9972988..9975946,2	K562	blood:
5	chr1:9885959..9887810-chr1:9888223..9890308,2	K562	blood:
6	chr1:9886240..9887970-chr1:9893394..9897363,3	K562	blood:

Variant related genes	Relation type
ENSG00000173614	Chromatin interaction
ENSG00000162441	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000223989	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10864436	0.90[EUR][1000 genomes]
rs11121492	0.94[EUR][1000 genomes]
rs11121493	0.86[EUR][1000 genomes]
rs11806520	0.80[EUR][1000 genomes]
rs12025864	0.84[AFR][1000 genomes]
rs12034239	0.83[EUR][1000 genomes]
rs12034313	0.83[AFR][1000 genomes]
rs12078414	0.80[EUR][1000 genomes]
rs12087051	0.83[EUR][1000 genomes]
rs1228434	0.86[EUR][1000 genomes]
rs1631962	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17034335	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17034340	0.94[EUR][1000 genomes]
rs1767271	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1767277	0.80[EUR][1000 genomes]
rs2788605	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41280776	0.86[ASN][1000 genomes]
rs4585981	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57560942	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59729812	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6699320	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855733	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855735	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855745	0.83[EUR][1000 genomes]
rs72855747	0.83[EUR][1000 genomes]
rs767762	0.80[EUR][1000 genomes]
rs935071	0.83[EUR][1000 genomes]
rs946277	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946278	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946279	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9884800-9887200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:9885000-9888000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:9885400-9887000	Enhancers	Pancreas	Pancrea
4	chr1:9885600-9886800	Weak transcription	Colonic Mucosa	Colon
5	chr1:9885600-9887000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:9885600-9894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:9885800-9887000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:9885800-9887000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:9885800-9887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:9885800-9887600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:9885800-9895200	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:9885800-9895600	Weak transcription	Spleen	Spleen
13	chr1:9885800-9896200	Weak transcription	Psoas Muscle	Psoas
14	chr1:9886000-9887200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:9886000-9887200	Enhancers	HepG2	liver
16	chr1:9886000-9887800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:9886000-9887800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:9886000-9887800	Weak transcription	Placenta	Placenta
19	chr1:9886000-9887800	Weak transcription	Fetal Thymus	thymus
20	chr1:9886000-9891200	Weak transcription	Esophagus	oesophagus
21	chr1:9886000-9893800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:9886000-9895600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:9886000-9895600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:9886000-9895600	Weak transcription	Right Atrium	heart
25	chr1:9886200-9887000	Enhancers	A549	lung
26	chr1:9886200-9887000	Enhancers	Hela-S3	cervix
27	chr1:9886200-9887200	Enhancers	HMEC	breast
28	chr1:9886200-9887600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:9886200-9887800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:9886200-9887800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:9886200-9887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:9886200-9887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:9886200-9887800	Weak transcription	Osteobl	bone
34	chr1:9886200-9891200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:9886200-9895400	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:9886400-9886800	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr1:9886400-9887600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:9886600-9886800	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links