Variant report

Variant	rs6710395
Chromosome Location	chr2:168339866-168339867
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1112983	0.92[EUR][1000 genomes]
rs11899757	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12105560	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1227120	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1238298	0.83[EUR][1000 genomes]
rs12466695	0.94[EUR][1000 genomes]
rs12478609	0.83[ASN][1000 genomes]
rs12989813	0.88[ASN][1000 genomes]
rs12990145	0.87[ASN][1000 genomes]
rs12996381	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032189	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1541889	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1583217	0.84[ASN][1000 genomes]
rs1653420	0.85[EUR][1000 genomes]
rs1653425	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1653430	0.85[EUR][1000 genomes]
rs16853634	0.84[ASN][1000 genomes]
rs16853644	0.84[ASN][1000 genomes]
rs16853648	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16853653	0.84[ASN][1000 genomes]
rs16853655	0.84[ASN][1000 genomes]
rs16853681	0.81[ASN][1000 genomes]
rs1730713	0.87[EUR][1000 genomes]
rs1730725	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1813255	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1919851	0.84[ASN][1000 genomes]
rs1919854	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1919855	0.86[EUR][1000 genomes]
rs1983514	0.92[EUR][1000 genomes]
rs2052982	0.86[ASN][1000 genomes]
rs35523753	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35580310	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35827395	0.90[EUR][1000 genomes]
rs4667955	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59149606	0.87[ASN][1000 genomes]
rs61416591	0.81[ASN][1000 genomes]
rs6433000	0.91[EUR][1000 genomes]
rs6725601	0.81[ASN][1000 genomes]
rs6731834	0.84[ASN][1000 genomes]
rs67321550	0.87[ASN][1000 genomes]
rs67697939	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7567362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][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	nsv491872	chr2:168220323-168737986	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv3388045	chr2:168289403-168424317	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6710395	GALNT3	cis	cerebellum	SCAN
rs6710395	SP5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:168337000-168340400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:168337000-168355400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:168337200-168348200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:168338200-168343600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:168338200-168348200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:168338200-168366000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:168338400-168340400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:168338400-168341000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:168338400-168349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:168338400-168352400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:168338600-168340000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:168338800-168340400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:168338800-168340600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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