Variant report

Variant	rs7015950
Chromosome Location	chr8:51306704-51306705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr8:51306261-51307207	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr8:51306524-51306958	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr8:51306597-51306978	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
SNTG1	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10086867	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10092399	0.91[JPT][hapmap]
rs10103047	0.91[JPT][hapmap]
rs10113812	0.91[JPT][hapmap]
rs10504100	0.83[CEU][hapmap]
rs10504103	0.83[CEU][hapmap]
rs10504106	1.00[CEU][hapmap];0.93[TSI][hapmap];1.00[EUR][1000 genomes]
rs1117213	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs1160764	0.91[JPT][hapmap]
rs1160795	0.91[JPT][hapmap]
rs11782140	0.83[CEU][hapmap]
rs11783674	0.85[ASN][1000 genomes]
rs11989809	1.00[EUR][1000 genomes]
rs12155652	0.99[EUR][1000 genomes]
rs12156091	0.83[CEU][hapmap]
rs12540980	0.83[CEU][hapmap]
rs12541707	1.00[EUR][1000 genomes]
rs12541772	0.91[JPT][hapmap]
rs12544425	0.83[CEU][hapmap]
rs12545003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12545927	0.84[CHB][hapmap]
rs12546829	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12547242	0.83[CEU][hapmap]
rs12548399	0.83[CEU][hapmap]
rs12675994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679464	0.89[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13248969	0.82[CHB][hapmap]
rs13251725	0.82[CHB][hapmap]
rs13257386	0.83[CEU][hapmap]
rs13257851	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13260021	0.82[CHB][hapmap]
rs13260506	0.83[CEU][hapmap]
rs13261341	0.83[CEU][hapmap]
rs13275607	0.83[JPT][hapmap]
rs13278343	0.91[CHB][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13282203	0.83[CEU][hapmap]
rs1375942	0.81[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.86[MKK][hapmap];0.83[ASN][1000 genomes]
rs1375944	0.81[JPT][hapmap]
rs1450124	0.91[JPT][hapmap]
rs1450131	0.83[CEU][hapmap]
rs1460437	0.91[JPT][hapmap]
rs1466128	0.83[CEU][hapmap]
rs1470680	0.83[CEU][hapmap]
rs1481471	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1548073	0.81[CEU][hapmap]
rs1597432	0.81[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs1597433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs16914780	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs16914781	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs17769846	0.83[CEU][hapmap]
rs17770910	0.90[CHB][hapmap]
rs1947254	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2044777	0.83[CEU][hapmap]
rs2044778	0.83[CEU][hapmap]
rs2219574	0.91[JPT][hapmap]
rs2923059	0.80[CEU][hapmap];0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs2923062	0.93[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs2957598	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2957599	0.82[CEU][hapmap]
rs2957600	0.93[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs2957601	0.93[ASW][hapmap];0.80[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs35063719	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4147344	0.92[CHB][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs4242460	1.00[ASN][1000 genomes]
rs4256602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4263785	0.83[CEU][hapmap]
rs4292700	0.92[CHB][hapmap];0.84[CHD][hapmap];0.84[ASN][1000 genomes]
rs4339654	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364645	1.00[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[LWK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4379460	0.83[CEU][hapmap]
rs4410921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529480	1.00[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[LWK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4534138	0.81[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.98[ASN][1000 genomes]
rs4604450	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639524	0.80[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4873141	0.91[JPT][hapmap]
rs4873143	0.91[JPT][hapmap]
rs4873438	0.91[JPT][hapmap]
rs4873439	0.91[JPT][hapmap]
rs4873443	0.91[JPT][hapmap]
rs4873453	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6473114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6994415	0.82[ASN][1000 genomes]
rs6995334	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs7003725	0.91[JPT][hapmap]
rs7005672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7816983	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7820992	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7839253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7845433	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs896023	0.83[CEU][hapmap]
rs930671	0.83[CEU][hapmap]
rs9643720	0.91[JPT][hapmap]
rs983055	0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv948436	chr8:51115028-51917504	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv831312	chr8:51239772-51422844	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7015950	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:51300000-51319800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:51306400-51306800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr8:51306400-51306800	Enhancers	Fetal Brain Female	brain
4	chr8:51306400-51309000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:51306600-51307200	Enhancers	Fetal Stomach	stomach

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