Variant report

Variant	rs10256635
Chromosome Location	chr7:70778948-70778949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10226199	0.93[EUR][1000 genomes]
rs10231965	0.80[EUR][1000 genomes]
rs10261998	0.87[EUR][1000 genomes]
rs10263619	0.91[EUR][1000 genomes]
rs10266560	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes]
rs10272997	0.94[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs11970929	0.85[ASN][1000 genomes]
rs11976781	0.84[EUR][1000 genomes]
rs12666910	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12668780	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12669285	0.93[EUR][1000 genomes]
rs12673556	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1574440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1922527	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs2141885	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2527289	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2527291	0.86[ASN][1000 genomes]
rs2527297	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2527298	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.82[ASN][1000 genomes]
rs2527312	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs28670821	0.85[EUR][1000 genomes]
rs2867411	0.92[EUR][1000 genomes]
rs28799658	0.90[EUR][1000 genomes]
rs3923571	0.93[EUR][1000 genomes]
rs4073529	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6460649	0.88[EUR][1000 genomes]
rs67615560	0.87[EUR][1000 genomes]
rs6942815	0.85[EUR][1000 genomes]
rs6943983	0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs6961808	0.87[EUR][1000 genomes]
rs6976562	0.84[EUR][1000 genomes]
rs6976574	0.85[EUR][1000 genomes]
rs6976591	0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs73177835	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73179792	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181636	0.89[ASN][1000 genomes]
rs73181639	0.89[ASN][1000 genomes]
rs73181654	0.89[ASN][1000 genomes]
rs73181662	0.87[ASN][1000 genomes]
rs73181665	0.89[ASN][1000 genomes]
rs73181667	0.89[ASN][1000 genomes]
rs73181672	0.89[ASN][1000 genomes]
rs73181677	0.87[ASN][1000 genomes]
rs73193229	0.88[ASN][1000 genomes]
rs73193235	0.89[ASN][1000 genomes]
rs73356099	0.95[EUR][1000 genomes]
rs7778324	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7792223	0.81[EUR][1000 genomes]
rs7810163	0.87[ASN][1000 genomes]
rs7810482	0.89[ASN][1000 genomes]
rs7811052	0.89[ASN][1000 genomes]
rs9638618	0.82[GIH][hapmap]
rs9886302	0.82[CEU][hapmap];0.90[JPT][hapmap];0.85[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	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats 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 miRNA	6 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10256635	STAG3L4	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70765800-70790000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:70773400-70780800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:70773400-70789800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:70774000-70779800	Weak transcription	Fetal Stomach	stomach
5	chr7:70777000-70788800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:70777600-70779000	Enhancers	Colon Smooth Muscle	Colon
7	chr7:70778000-70779400	Enhancers	Rectal Smooth Muscle	rectum
8	chr7:70778200-70779200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr7:70778200-70779400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr7:70778200-70779400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr7:70778200-70779400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr7:70778200-70779600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:70778200-70779600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:70778400-70779000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr7:70778400-70779000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr7:70778400-70779000	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr7:70778400-70779000	Enhancers	Brain Germinal Matrix	brain
18	chr7:70778400-70779000	Enhancers	Fetal Lung	lung
19	chr7:70778400-70779200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr7:70778400-70779400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr7:70778400-70779400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr7:70778800-70779000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:70778800-70780200	Weak transcription	Fetal Muscle Leg	muscle
24	chr7:70778800-70784400	Weak transcription	Brain Anterior Caudate	brain

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