Variant report

Variant	rs6974522
Chromosome Location	chr7:39073372-39073373
allele	C/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	GATA3	chr7:39073222-39073404	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
POU6F2	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1000869	0.87[ASN][1000 genomes]
rs10248136	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs10464366	0.87[CHB][hapmap]
rs10951593	0.87[CHB][hapmap]
rs1116811	0.87[CHB][hapmap]
rs11765705	0.87[CHB][hapmap]
rs11972294	0.86[ASN][1000 genomes]
rs11973171	0.88[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs12532009	0.87[CHB][hapmap]
rs12538487	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12667652	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669446	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs12670003	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12671046	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[ASN][1000 genomes]
rs12674371	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13242896	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1525798	0.94[CHB][hapmap]
rs1527952	0.94[CHB][hapmap]
rs17171519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6462886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6462887	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6944670	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6945380	0.94[CHB][hapmap]
rs6952464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6979210	0.88[CHB][hapmap]
rs7779853	0.87[CHB][hapmap]
rs7785889	0.93[CHB][hapmap]
rs7801660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs940876	0.81[CHB][hapmap]

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	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv887967	chr7:39009307-39090698	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39067400-39073600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:39067400-39074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr7:39072000-39073600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr7:39072000-39075000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:39072200-39074000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:39072400-39083200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:39072800-39074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:39073000-39073800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr7:39073200-39073400	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links