Variant report

Variant	rs17777439
Chromosome Location	chr7:104502149-104502150
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57969077..57971164-chr7:104500909..104502928,2	MCF-7	breast:
2	chr7:103845618..103848570-chr7:104501714..104504552,2	K562	blood:

Variant related genes	Relation type
ENSG00000108443	Chromatin interaction
ENSG00000164815	Chromatin interaction
ENSG00000108423	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10216243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10226456	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10226802	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227564	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10235696	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10236552	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10237433	0.86[CHB][hapmap]
rs10238498	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10243336	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10243529	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10247246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253341	0.90[CHB][hapmap]
rs10257360	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10259925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10262655	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10264318	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10272668	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10273609	0.82[ASN][1000 genomes]
rs10274240	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10280365	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10281485	0.85[EUR][1000 genomes]
rs10953454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953455	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670275	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12672211	0.86[CHB][hapmap]
rs12705281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12705282	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12705285	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13233998	0.86[EUR][1000 genomes]
rs1468813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17777379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285533	0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28546781	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28587189	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34083033	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34171467	0.85[EUR][1000 genomes]
rs34439336	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34508498	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35146170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35324592	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35337480	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35756879	0.85[EUR][1000 genomes]
rs35894637	0.87[ASN][1000 genomes]
rs35988800	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4351347	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6949139	0.85[CHB][hapmap]
rs6963979	0.89[CHB][hapmap];0.86[ASN][1000 genomes]
rs6968540	0.84[ASN][1000 genomes]
rs71562620	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71562621	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71562626	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7781864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104476400-104503000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr7:104481600-104514400	Weak transcription	Fetal Kidney	kidney
3	chr7:104494000-104502800	Weak transcription	Fetal Intestine Large	intestine
4	chr7:104499400-104502200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:104499400-104502200	Weak transcription	GM12878-XiMat	blood
6	chr7:104501400-104503000	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:104501600-104502200	Enhancers	Fetal Heart	heart
8	chr7:104501600-104503200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:104501600-104503400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:104501600-104504800	Strong transcription	Fetal Intestine Small	intestine
11	chr7:104501800-104503200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr7:104502000-104502400	Enhancers	Primary T cells from cord blood	blood
13	chr7:104502000-104503000	Enhancers	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links