Variant report

Variant	rs3935607
Chromosome Location	chr1:246962909-246962910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12069800	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12079867	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12117291	0.86[EUR][1000 genomes]
rs12120124	0.85[EUR][1000 genomes]
rs12122102	0.87[CEU][hapmap];0.83[MEX][hapmap];0.86[EUR][1000 genomes]
rs12566739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[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];0.95[ASN][1000 genomes]
rs4926446	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4926462	0.96[CEU][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4926464	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7522479	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv873421	chr1:246818634-247044692	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv430413	chr1:246845971-246975015	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv873422	chr1:246854862-247002638	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv1006262	chr1:246892826-246964775	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv523531	chr1:246893948-246967899	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv999756	chr1:246894542-246969660	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv1009436	chr1:246910373-246965832	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv873423	chr1:246923861-246978504	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
14	nsv549545	chr1:246936353-246963019	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv525154	chr1:246954166-246963019	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3935607	SCCPDH	cis	cerebellum	SCAN
rs3935607	LOC149134	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246958400-246966800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:246960000-246964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:246961000-246963400	Enhancers	Fetal Muscle Leg	muscle
4	chr1:246961600-246963000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr1:246961800-246963000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:246962000-246963200	Enhancers	Fetal Heart	heart
7	chr1:246962200-246963000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:246962200-246963400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:246962400-246963000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:246962400-246963000	Enhancers	Brain Angular Gyrus	brain
11	chr1:246962400-246963000	Enhancers	Fetal Brain Male	brain
12	chr1:246962400-246963000	Enhancers	Fetal Intestine Small	intestine
13	chr1:246962400-246963200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:246962400-246963200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr1:246962400-246963400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr1:246962400-246964000	Weak transcription	HSMM	muscle
17	chr1:246962400-246965800	Weak transcription	Placenta	Placenta
18	chr1:246962600-246963000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:246962600-246963000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:246962600-246963000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr1:246962600-246963000	Flanking Active TSS	Brain Substantia Nigra	brain
22	chr1:246962600-246963000	Enhancers	Fetal Brain Female	brain
23	chr1:246962600-246963600	Bivalent Enhancer	HepG2	liver
24	chr1:246962600-246964400	Weak transcription	HSMMtube	muscle
25	chr1:246962800-246963000	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr1:246962800-246963000	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:246962800-246963200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:246962800-246965800	Weak transcription	Right Ventricle	heart

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