Variant report

Variant	rs2215141
Chromosome Location	chr7:108244234-108244235
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108243393..108246050-chr7:108248845..108250724,2	K562	blood:
2	chr7:108234971..108237051-chr7:108243040..108246034,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1029707	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1029708	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767037	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11767071	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773524	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11773875	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17341955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17426638	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108731	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505662	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4298438	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55760662	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58954269	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466244	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67940245	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945788	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6949766	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951751	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs726608	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727881	0.81[EUR][1000 genomes]
rs7790890	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795236	0.81[EUR][1000 genomes]
rs9690171	0.82[EUR][1000 genomes]
rs975124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9768342	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9918599	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2215141	NRCAM	cis	cerebellum	SCAN
rs2215141	THAP5	cis	lymphoblastoid	seeQTL
rs2215141	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108240400-108244400	Weak transcription	Brain Germinal Matrix	brain
2	chr7:108240400-108245600	Weak transcription	Fetal Brain Male	brain
3	chr7:108243000-108245400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:108243600-108244800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:108243600-108246200	Enhancers	Placenta	Placenta
6	chr7:108243800-108244400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:108244000-108244600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr7:108244000-108244600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:108244000-108244800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:108244000-108245000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr7:108244000-108245800	Enhancers	Fetal Brain Female	brain
12	chr7:108244200-108244600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:108244200-108244600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr7:108244200-108244600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr7:108244200-108244600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr7:108244200-108244600	Enhancers	Cortex derived primary cultured neurospheres	brain

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