Variant report

Variant	rs2544769
Chromosome Location	chr5:96476135-96476136
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96381504..96384488-chr5:96474189..96476207,2	K562	blood:
2	chr5:96270867..96272370-chr5:96475978..96478536,2	MCF-7	breast:
3	chr5:96469286..96471593-chr5:96474372..96477073,2	K562	blood:

Variant related genes	Relation type
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10039917	0.87[ASN][1000 genomes]
rs10043135	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs10071737	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1035507	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10463198	0.80[CHB][hapmap]
rs11954059	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs12520374	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13167790	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs182625	0.82[ASN][1000 genomes]
rs2287903	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316178	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316190	0.86[ASN][1000 genomes]
rs316201	0.96[CEU][hapmap];0.95[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316202	0.92[CEU][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs316203	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316204	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316205	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316213	0.80[CHB][hapmap]
rs316217	0.87[ASN][1000 genomes]
rs316218	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs316219	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs316232	0.82[ASN][1000 genomes]
rs316233	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs316234	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs444243	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7717829	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	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv830413	chr5:96450582-96509294	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
6	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96455400-96491800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:96456400-96478000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:96459800-96491800	Weak transcription	Primary B cells from cord blood	blood
4	chr5:96471200-96476200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:96472000-96476200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:96472000-96476200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:96472000-96476800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:96473000-96476400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:96474000-96476400	Weak transcription	Brain Germinal Matrix	brain
10	chr5:96474200-96476200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:96475000-96476200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:96475000-96476200	Weak transcription	Brain Substantia Nigra	brain
13	chr5:96475000-96478200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:96475200-96476200	Enhancers	Brain Hippocampus Middle	brain
15	chr5:96475200-96477000	Enhancers	Fetal Brain Female	brain
16	chr5:96475200-96480000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:96475400-96477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:96475400-96478000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:96475600-96476600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:96475800-96476200	Enhancers	Fetal Muscle Leg	muscle
21	chr5:96475800-96476400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr5:96475800-96476400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:96476000-96476600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:96476000-96476800	Weak transcription	Fetal Brain Male	brain
25	chr5:96476000-96478000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:96476000-96478400	Active TSS	Brain Anterior Caudate	brain
27	chr5:96476000-96478600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links