Variant report

Variant	rs56288561
Chromosome Location	chr1:173883517-173883518
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173834428..173840700-chr1:173878764..173885322,14	MCF-7	breast:
2	chr1:173835651..173839404-chr1:173878959..173883807,5	K562	blood:
3	chr1:173882932..173886692-chr1:173886862..173890895,4	K562	blood:
4	chr1:173832843..173835312-chr1:173882072..173883606,2	K562	blood:
5	chr1:173862229..173864834-chr1:173882174..173883683,2	K562	blood:
6	chr1:173835088..173837217-chr1:173882626..173885539,2	K562	blood:
7	chr1:173831929..173834882-chr1:173882309..173883868,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000252231	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000208317	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10489894	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535527	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846529	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16846541	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17359906	0.89[ASN][1000 genomes]
rs1969757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227607	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227609	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2295957	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35571466	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56064477	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56382804	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59675210	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61609614	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61827869	0.86[ASN][1000 genomes]
rs6667813	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6682076	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6698314	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6700754	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711419	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711421	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711423	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72711425	1.00[ASN][1000 genomes]
rs7525115	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:173857400-173884400	Weak transcription	HepG2	liver
4	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
6	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
7	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
8	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:173870000-173898000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:173870400-173887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
13	chr1:173872400-173896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
15	chr1:173876400-173884000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:173879000-173883800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:173879200-173899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:173882800-173885400	Weak transcription	K562	blood
19	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:173883200-173884400	Transcr. at gene 5' and 3'	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links