Variant report

Variant	rs7742134
Chromosome Location	chr6:114388111-114388112
allele	C/T
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	chr6:114388069-114388361	PFSK-1	brain:	n/a	n/a
2	GATA2	chr6:114388063-114388424	SH-SY5Y	brain:	n/a	chr6:114388088-114388098 chr6:114388225-114388232 chr6:114388224-114388234 chr6:114388225-114388232 chr6:114388225-114388232 chr6:114388139-114388146 chr6:114388218-114388239

Variant related genes	Relation type
HS3ST5	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10782177	1.00[ASN][1000 genomes]
rs1157989	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11967410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11970460	0.88[ASN][1000 genomes]
rs12190983	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12201726	1.00[ASN][1000 genomes]
rs12201804	1.00[ASN][1000 genomes]
rs12203341	1.00[ASN][1000 genomes]
rs12207338	0.91[ASN][1000 genomes]
rs12211751	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12211928	0.91[ASN][1000 genomes]
rs12213853	0.91[ASN][1000 genomes]
rs17191369	0.88[ASN][1000 genomes]
rs1961955	1.00[ASN][1000 genomes]
rs62418080	1.00[ASN][1000 genomes]
rs7743208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7753206	1.00[ASN][1000 genomes]
rs7764690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9320479	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[ASN][1000 genomes]
rs9481418	0.91[ASN][1000 genomes]
rs9481421	0.88[ASN][1000 genomes]
rs9488328	0.88[ASN][1000 genomes]
rs9488329	0.88[ASN][1000 genomes]
rs9488334	0.88[ASN][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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1024062	chr6:114311029-114679557	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7742134	RWDD1	cis	parietal	SCAN
rs7742134	FAM162B	cis	cerebellum	SCAN
rs7742134	TRAF3IP2	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114370200-114389600	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:114371400-114388200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:114379600-114390400	Weak transcription	HepG2	liver
4	chr6:114383400-114390000	Weak transcription	Brain Germinal Matrix	brain
5	chr6:114384000-114389600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:114384200-114389400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:114384200-114389400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:114384200-114389600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:114384200-114389600	Weak transcription	Brain Substantia Nigra	brain
10	chr6:114384200-114390000	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:114384200-114398200	Weak transcription	Brain Angular Gyrus	brain
12	chr6:114385600-114415800	Weak transcription	HSMM	muscle
13	chr6:114385800-114389600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:114386200-114388200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:114386400-114396600	Weak transcription	HSMMtube	muscle
16	chr6:114386600-114397800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:114387200-114388200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:114387200-114389600	Weak transcription	Brain Anterior Caudate	brain
19	chr6:114388000-114388400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:114388000-114388400	Enhancers	Psoas Muscle	Psoas
21	chr6:114388000-114389000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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