Variant report

Variant	rs11871785
Chromosome Location	chr17:59761706-59761707
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59759785..59761947-chr20:55840285..55842143,2	MCF-7	breast:
2	chr17:59760845..59762772-chr17:59875907..59878098,2	MCF-7	breast:
3	chr17:59761545..59763933-chr17:59805330..59807070,2	MCF-7	breast:
4	chr1:121483386..121485225-chr17:59760581..59762463,2	MCF-7	breast:
5	chr17:59760945..59762939-chr17:59764164..59767018,2	K562	blood:

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11079451	0.95[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs11079454	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654606	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11867566	0.85[ASN][1000 genomes]
rs2007931	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2040609	0.91[CHB][hapmap]
rs2106663	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2158005	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159451	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35090865	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35524448	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4988357	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]
rs56218811	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62071871	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62071872	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6504058	0.82[CHB][hapmap]
rs6504065	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67223644	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7214703	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7219555	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7220740	0.87[ASN][1000 genomes]
rs7222482	0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs8064683	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9908115	0.95[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs9912366	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9915787	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9916777	0.80[AMR][1000 genomes]
rs9916780	0.84[AMR][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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11871785	AKAP1	cis	cerebellum	SCAN
rs11871785	VEZF1	cis	parietal	SCAN
rs11871785	RNF43	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59751000-59777200	Weak transcription	HepG2	liver
2	chr17:59755600-59778000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:59756600-59772600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:59756600-59777000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr17:59757000-59765400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr17:59757000-59772000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr17:59757400-59775600	Weak transcription	A549	lung
8	chr17:59758400-59772400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:59758600-59765400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:59758600-59766800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr17:59758600-59768800	Weak transcription	Fetal Intestine Small	intestine
12	chr17:59759400-59762800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:59759400-59763000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:59759400-59767000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr17:59759400-59772000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr17:59759400-59772400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr17:59759600-59771200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr17:59759800-59765200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr17:59759800-59769200	Weak transcription	Thymus	Thymus
20	chr17:59759800-59775400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:59759800-59776600	Weak transcription	GM12878-XiMat	blood
22	chr17:59760000-59761800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:59760000-59763200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:59760000-59763400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:59760200-59765200	Weak transcription	Fetal Thymus	thymus
26	chr17:59760200-59774000	Weak transcription	Hela-S3	cervix
27	chr17:59760600-59763400	Strong transcription	NH-A	brain
28	chr17:59760800-59765200	Weak transcription	Fetal Stomach	stomach
29	chr17:59760800-59767600	Strong transcription	Dnd41	blood
30	chr17:59761000-59765600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr17:59761000-59766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:59761200-59772800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr17:59761400-59771600	Weak transcription	NHDF-Ad	bronchial
34	chr17:59761400-59776000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr17:59761600-59766600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:59761600-59767200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:59761600-59776200	Weak transcription	HUVEC	blood vessel

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