Variant report

Variant	rs4893863
Chromosome Location	chr2:179887705-179887706
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10084229	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10164814	0.88[JPT][hapmap]
rs10188759	0.90[JPT][hapmap]
rs10803924	1.00[JPT][hapmap]
rs10930852	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930855	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10930856	1.00[CHB][hapmap]
rs12693175	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12693179	0.90[JPT][hapmap]
rs12997079	1.00[CHB][hapmap]
rs13022867	1.00[CHB][hapmap]
rs13029576	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13382185	0.90[JPT][hapmap]
rs13396334	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs13404037	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1354385	0.95[ASN][1000 genomes]
rs173110	0.92[ASN][1000 genomes]
rs17363260	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs17363267	1.00[CHB][hapmap]
rs2289993	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2289994	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2592564	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655158	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs340321	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs340326	0.88[ASN][1000 genomes]
rs340328	0.95[ASN][1000 genomes]
rs340329	0.84[ASN][1000 genomes]
rs340332	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs340334	0.80[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340338	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340349	0.95[ASN][1000 genomes]
rs340350	0.95[ASN][1000 genomes]
rs6433746	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558039	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598203	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601366	0.89[JPT][hapmap]
rs924801	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875455	chr2:179732845-179909467	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv875456	chr2:179775893-179896787	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv875459	chr2:179839833-179896787	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv875460	chr2:179843612-179896787	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv875461	chr2:179843612-179900720	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv875462	chr2:179843612-179901443	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv875463	chr2:179843612-179909467	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv875464	chr2:179843612-179939493	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv875465	chr2:179843612-179966804	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv875466	chr2:179856777-179909467	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4893863	PPP1R1C	cis	cerebellum	SCAN
rs4893863	AMD1	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179883600-179889000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:179884000-179889000	Weak transcription	Primary T cells from cord blood	blood
3	chr2:179884600-179890400	Enhancers	Primary B cells from peripheral blood	blood
4	chr2:179886000-179896000	Weak transcription	HSMMtube	muscle
5	chr2:179886200-179888600	Weak transcription	Psoas Muscle	Psoas
6	chr2:179886400-179889000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:179886400-179892800	Weak transcription	Right Atrium	heart
8	chr2:179886800-179887800	Flanking Active TSS	Fetal Heart	heart
9	chr2:179886800-179888000	Enhancers	Brain Germinal Matrix	brain
10	chr2:179887000-179890400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr2:179887200-179887800	Enhancers	Right Ventricle	heart
12	chr2:179887200-179888800	Weak transcription	Primary B cells from cord blood	blood
13	chr2:179887200-179888800	Enhancers	Left Ventricle	heart
14	chr2:179887400-179887800	Enhancers	Brain Angular Gyrus	brain
15	chr2:179887600-179887800	Enhancers	Pancreas	Pancrea
16	chr2:179887600-179889000	Enhancers	GM12878-XiMat	blood
17	chr2:179887600-179890600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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