Variant report

Variant	rs34655504
Chromosome Location	chr7:71616704-71616705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10215588	0.83[JPT][hapmap]
rs10224431	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10231333	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs10251441	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10252717	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs10254309	0.83[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap]
rs10255136	0.83[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap]
rs10260183	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10260420	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10260767	1.00[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10274714	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10280044	0.93[ASN][1000 genomes]
rs10281262	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10434994	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10807742	0.83[JPT][hapmap]
rs10807743	0.93[ASN][1000 genomes]
rs10807744	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs10950291	0.82[JPT][hapmap]
rs10950294	0.83[JPT][hapmap]
rs10950295	0.83[JPT][hapmap]
rs10950297	0.83[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap]
rs10950298	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs10950301	0.85[ASN][1000 genomes]
rs11764286	0.81[YRI][hapmap]
rs11765179	0.83[JPT][hapmap]
rs11767811	0.82[ASN][1000 genomes]
rs11772246	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs11773728	0.81[ASN][1000 genomes]
rs11972568	0.94[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11976625	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11982267	0.83[JPT][hapmap]
rs11983124	0.83[JPT][hapmap]
rs12531663	0.89[JPT][hapmap]
rs12666578	0.83[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap]
rs12668623	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12668647	0.91[EUR][1000 genomes]
rs12673109	0.91[GIH][hapmap];0.90[JPT][hapmap]
rs12699123	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12699124	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13224539	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs13235059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13239589	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs16869610	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17144369	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17144373	0.83[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2040869	0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2040870	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2079318	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2867567	0.83[CHB][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap]
rs2867604	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34310597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34801868	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35585314	0.84[MEX][hapmap]
rs4457209	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4717628	0.85[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs4719207	0.83[JPT][hapmap]
rs4719209	0.83[JPT][hapmap]
rs4719215	0.84[ASN][1000 genomes]
rs4719216	0.83[JPT][hapmap]
rs6952558	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs6959686	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs6963114	0.83[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap]
rs71551251	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73704307	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7797796	0.83[JPT][hapmap]
rs7799436	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1015848	chr7:71552185-71736068	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv538942	chr7:71552185-71736068	ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv831024	chr7:71569349-71735250	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1023496	chr7:71593461-71633053	Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv529620	chr7:71604785-71935721	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34655504	STX1A	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71607600-71617600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:71614600-71619600	Enhancers	Brain Anterior Caudate	brain
3	chr7:71614600-71619800	Enhancers	Brain Substantia Nigra	brain
4	chr7:71614800-71617200	Enhancers	Brain Cingulate Gyrus	brain
5	chr7:71614800-71617400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr7:71615000-71617400	Enhancers	Brain Hippocampus Middle	brain
7	chr7:71615400-71619000	Enhancers	Pancreas	Pancrea
8	chr7:71615400-71619600	Enhancers	Brain Angular Gyrus	brain
9	chr7:71615800-71616800	ZNF genes & repeats	Dnd41	blood
10	chr7:71616000-71619200	Enhancers	Fetal Thymus	thymus
11	chr7:71616600-71617400	Enhancers	Thymus	Thymus
12	chr7:71616600-71618800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr7:71616600-71619200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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