Variant report

Variant	rs11977597
Chromosome Location	chr7:100916665-100916666
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	POLR2A	chr7:100915583-100917178	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:100887858..100889403-chr7:100915187..100917506,2	K562	blood:
2	chr7:100912998..100915011-chr7:100915774..100918706,2	K562	blood:

Variant related genes	Relation type
RNU6-1104P	TF binding region
ENSG00000214253	Chromatin interaction
ENSG00000207454	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10250685	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs1047319	0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap]
rs11769624	0.92[JPT][hapmap]
rs11971737	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11977513	0.95[ASN][1000 genomes]
rs12670262	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs17319250	0.92[JPT][hapmap]
rs2072168	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs2302428	0.83[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs3757460	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]

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	nsv831075	chr7:100692297-100917018	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1030604	chr7:100717732-101223465	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv2422376	chr7:100743485-101016471	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv464651	chr7:100792810-100971604	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv607974	chr7:100792810-100971604	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv429788	chr7:100799565-101178565	Weak transcription Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	esv2752134	chr7:100800131-101141867	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv831076	chr7:100828847-101011674	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv888819	chr7:100833153-100920007	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2422326	chr7:100833449-101000131	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv607978	chr7:100861213-100971604	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv831077	chr7:100874209-101083930	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv1023393	chr7:100904333-101102046	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv970917	chr7:100907928-100928609	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11977597	MYST3	trans	parietal	SCAN
rs11977597	EMID2	cis	cerebellum	SCAN
rs11977597	TAC1	cis	parietal	SCAN
rs11977597	VGF	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100914600-100921400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:100915000-100917400	Enhancers	Brain Germinal Matrix	brain
3	chr7:100916000-100917000	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr7:100916000-100917200	Enhancers	H9 Cell Line	embryonic stem cell
5	chr7:100916000-100917200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:100916000-100917200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:100916000-100917400	Enhancers	H1 Cell Line	embryonic stem cell
8	chr7:100916000-100917400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:100916000-100917400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr7:100916200-100916800	Enhancers	Brain Cingulate Gyrus	brain
11	chr7:100916200-100917000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:100916200-100917000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr7:100916200-100917200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr7:100916200-100917200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:100916200-100917200	Bivalent Enhancer	Brain Hippocampus Middle	brain
16	chr7:100916200-100917400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr7:100916200-100918200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:100916200-100924800	Strong transcription	Liver	Liver
19	chr7:100916400-100916800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:100916600-100916800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr7:100916600-100916800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr7:100916600-100917000	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr7:100916600-100917000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:100916600-100917000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr7:100916600-100925800	Weak transcription	Brain Angular Gyrus	brain

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