Variant report

Variant	rs6554200
Chromosome Location	chr4:55529409-55529410
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:55526044..55527656-chr4:55529218..55531772,2	MCF-7	breast:
2	chr4:55481868..55484293-chr4:55528991..55530564,2	K562	blood:
3	chr4:55522620..55525465-chr4:55527232..55529578,3	K562	blood:

Variant related genes	Relation type
ENSG00000157404	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10488849	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11727273	0.94[EUR][1000 genomes]
rs11940731	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12499367	0.90[EUR][1000 genomes]
rs12504135	0.90[EUR][1000 genomes]
rs2159935	0.82[ASN][1000 genomes]
rs2192158	0.90[EUR][1000 genomes]
rs2192159	0.90[EUR][1000 genomes]
rs2237029	0.96[ASN][1000 genomes]
rs2237030	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237037	0.88[CEU][hapmap]
rs2237038	0.91[CEU][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2855778	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819391	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819393	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554193	0.90[EUR][1000 genomes]
rs6554194	0.90[EUR][1000 genomes]
rs6554199	0.91[CEU][hapmap]
rs6815651	0.84[EUR][1000 genomes]
rs6825293	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7679314	0.81[EUR][1000 genomes]
rs7695300	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs981959	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999020	0.91[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999021	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55525800-55537200	Weak transcription	Right Atrium	heart
2	chr4:55526600-55531600	Weak transcription	Gastric	stomach
3	chr4:55527400-55529600	Enhancers	Primary hematopoietic stem cells	blood
4	chr4:55527800-55530000	Enhancers	NHDF-Ad	bronchial
5	chr4:55527800-55532200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:55528200-55529800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:55528400-55530200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:55528600-55529800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:55528600-55529800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:55528600-55529800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:55528600-55529800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:55528600-55533400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:55528600-55534000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:55528600-55535400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:55529000-55530200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr4:55529000-55530400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr4:55529200-55529800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr4:55529200-55530200	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr4:55529200-55530400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr4:55529200-55530400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:55529200-55530600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr4:55529400-55529600	Enhancers	H1 Cell Line	embryonic stem cell
23	chr4:55529400-55529600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr4:55529400-55530200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:55529400-55530400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:55529400-55530800	Enhancers	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links