Variant report

Variant	rs13226410
Chromosome Location	chr7:71177797-71177798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10085425	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085521	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs10085628	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085829	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226321	0.90[CEU][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]
rs10226346	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227562	1.00[CHD][hapmap]
rs10231977	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233708	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236650	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236708	0.85[AFR][1000 genomes]
rs10241679	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250033	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254113	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256029	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256176	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265610	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10266865	0.81[AFR][1000 genomes]
rs10278031	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282319	0.83[AFR][1000 genomes]
rs10282695	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973569	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973697	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12112718	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12113685	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525720	1.00[CHD][hapmap]
rs2109730	0.87[AFR][1000 genomes]
rs2867506	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34074787	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34219989	1.00[ASN][1000 genomes]
rs35325385	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35656749	0.86[EUR][1000 genomes]
rs35848034	1.00[ASN][1000 genomes]
rs473362	0.88[CEU][hapmap]
rs492162	1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs496833	0.89[EUR][1000 genomes]
rs55812691	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55882044	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61193840	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943205	0.87[AFR][1000 genomes]
rs6970747	0.81[EUR][1000 genomes]
rs7786574	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788085	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788255	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv516049	chr7:71026463-71280299	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1019799	chr7:71027947-71274161	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv538938	chr7:71027947-71274161	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1016182	chr7:71033825-71285800	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1034811	chr7:71033825-71288961	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1024288	chr7:71039619-71285800	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1027835	chr7:71055226-71281334	Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv538939	chr7:71055226-71281334	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1026364	chr7:71055226-71287960	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv538940	chr7:71055226-71287960	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv948337	chr7:71057204-71277518	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1027496	chr7:71162362-71575116	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13226410	LIMK1	cis	cerebellum	SCAN
rs13226410	WBSCR17	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71173000-71197400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:71174000-71181400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:71174200-71179800	Weak transcription	Right Atrium	heart
4	chr7:71174200-71181600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr7:71174800-71181200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:71175200-71181400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr7:71175400-71185000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:71175600-71178600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:71175600-71178600	Strong transcription	Ovary	ovary
10	chr7:71175800-71179800	Weak transcription	Pancreas	Pancrea
11	chr7:71175800-71181000	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:71176000-71187200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr7:71176800-71179800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:71176800-71181000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:71177000-71177800	Strong transcription	Aorta	Aorta
16	chr7:71177000-71178000	Strong transcription	Fetal Muscle Leg	muscle
17	chr7:71177400-71178400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:71177400-71178600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:71177600-71178000	Enhancers	Right Ventricle	heart
20	chr7:71177600-71178200	Enhancers	Fetal Heart	heart
21	chr7:71177600-71178600	Strong transcription	Fetal Muscle Trunk	muscle

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