Variant report

Variant	rs12977527
Chromosome Location	chr19:42467607-42467608
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	chr19:42466954-42467765	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr19:42466845-42467806	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42461956..42463771-chr19:42465748..42467644,2	K562	blood:

Variant related genes	Relation type
RABAC1	TF binding region
ENSG00000105404	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1075728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35287851	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs891167	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12977527	SLC1A5	cis	parietal	SCAN
rs12977527	IGFL1	cis	parietal	SCAN
rs12977527	SNORD32A	cis	parietal	SCAN
rs12977527	PVR	cis	parietal	SCAN
rs12977527	TMEM143	cis	parietal	SCAN
rs12977527	RABAC1	cis	Whole Blood	GTEx
rs12977527	EHD2	cis	parietal	SCAN
rs12977527	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42464000-42469400	Weak transcription	Thymus	Thymus
2	chr19:42464000-42470200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:42464000-42470200	Weak transcription	Left Ventricle	heart
4	chr19:42464000-42470400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:42464000-42471400	Weak transcription	Right Ventricle	heart
6	chr19:42464000-42482000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:42464000-42485400	Weak transcription	Primary T cells from cord blood	blood
8	chr19:42464000-42485400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:42464000-42486600	Weak transcription	Right Atrium	heart
10	chr19:42464000-42495000	Weak transcription	Fetal Brain Male	brain
11	chr19:42464200-42468600	Weak transcription	Fetal Thymus	thymus
12	chr19:42464200-42470000	Weak transcription	Fetal Brain Female	brain
13	chr19:42464200-42470200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:42464200-42470200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr19:42464200-42470200	Weak transcription	Dnd41	blood
16	chr19:42464200-42470400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:42464200-42470400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:42464200-42470400	Weak transcription	Brain Germinal Matrix	brain
19	chr19:42464200-42470400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:42464200-42470400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr19:42464200-42470600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:42464200-42471000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:42464200-42472000	Weak transcription	Brain Angular Gyrus	brain
24	chr19:42464200-42472600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:42464200-42473800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:42464200-42473800	Weak transcription	Brain Anterior Caudate	brain
27	chr19:42464200-42479600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr19:42464200-42485400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:42464200-42485400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:42464200-42489400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:42464200-42491000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:42464200-42491200	Weak transcription	Fetal Heart	heart
33	chr19:42464200-42493800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr19:42464200-42495000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:42464200-42497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr19:42464200-42497400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr19:42465600-42469200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:42467400-42467800	Enhancers	Esophagus	oesophagus
39	chr19:42467600-42470400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:42467600-42475600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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