Variant report

Variant	rs41900
Chromosome Location	chr7:117885737-117885738
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117874784..117876753-chr7:117884123..117886135,2	K562	blood:
2	chr7:117884617..117887581-chr7:117888612..117890526,2	MCF-7	breast:
3	chr7:117884069..117886965-chr7:117888003..117890494,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10085904	0.95[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs10226152	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10227326	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10229589	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10241875	0.83[EUR][1000 genomes]
rs10252627	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10267938	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10487390	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054032	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1061731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953864	0.87[EUR][1000 genomes]
rs1117254	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11486992	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11543742	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11770353	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11979012	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12112697	0.86[CEU][hapmap]
rs12537795	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12667103	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12673046	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13224733	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2041527	0.82[CEU][hapmap]
rs2058416	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058417	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2191920	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2402322	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2896242	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3802012	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4141028	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41901	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41902	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41905	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41906	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41908	0.83[EUR][1000 genomes]
rs41909	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41910	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41911	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41915	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41916	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41926	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41933	0.90[EUR][1000 genomes]
rs41934	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41935	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41938	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41939	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41945	0.82[EUR][1000 genomes]
rs41960	0.86[EUR][1000 genomes]
rs5002233	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6942513	0.86[CEU][hapmap]
rs6944524	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6946855	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6948096	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6956486	0.87[EUR][1000 genomes]
rs6964911	0.90[CEU][hapmap];0.84[CHB][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965144	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7779933	0.87[EUR][1000 genomes]
rs7796145	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7796148	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7797855	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7799229	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs7806490	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs917761	0.89[EUR][1000 genomes]
rs9655829	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9656260	0.87[EUR][1000 genomes]
rs979652	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.97[LWK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs989899	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs992035	0.82[CEU][hapmap]

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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv889089	chr7:117865940-117921267	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv889090	chr7:117865940-118067460	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41900	NAA38	cis	lymphoblastoid	seeQTL
rs41900	LSM8	cis	multi-tissue	Pritchard
rs41900	ANKRD7	cis	parietal	SCAN
rs41900	ANKRD7	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117884800-117886400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr7:117885000-117886200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:117885000-117886200	Enhancers	Dnd41	blood
4	chr7:117885200-117885800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:117885200-117885800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:117885200-117885800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:117885200-117886000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:117885200-117886000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links