Variant report

Variant	rs592420
Chromosome Location	chr8:9760420-9760421
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	SIN3A	chr8:9759698-9764536	H1-hESC	embryonic stem cell:	n/a	chr8:9764123-9764136 chr8:9761549-9761560 chr8:9761633-9761646 chr8:9762434-9762445 chr8:9760165-9760174
2	POLR2A	chr8:9759984-9760593	HL-60	blood:	n/a	n/a
3	POLR2A	chr8:9759634-9765032	H1-neurons	neurons:	n/a	n/a
4	SPI1	chr8:9759988-9760571	HL-60	blood:	n/a	chr8:9760156-9760163
5	ZNF263	chr8:9759669-9760782	HEK293-T-REx	kidney:	n/a	chr8:9759782-9759791 chr8:9760391-9760400
6	POLR2A	chr8:9758404-9764972	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr8:9760072-9760597	HL-60	blood:	n/a	n/a
8	MXI1	chr8:9759530-9764640	SK-N-SH	brain:	n/a	n/a
9	REST	chr8:9759431-9765302	H1-neurons	neurons:	n/a	chr8:9763658-9763671 chr8:9760877-9760897 chr8:9761543-9761556 chr8:9764262-9764271 chr8:9761633-9761646
10	CHD2	chr8:9760234-9761256	H1-hESC	embryonic stem cell:	n/a	chr8:9760797-9760807

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1L1-5	chr8:9757574-9760907	ENSG00000253230
2	lnc-RP1L1-5	chr8:9758199-9760839	ENSG00000253230
3	lnc-RP1L1-5	chr8:9758199-9760888	NONHSAT124969
4	lnc-RP1L1-5	chr8:9758199-9760897	NONHSAT124970
5	lnc-RP1L1-5	chr8:9758065-9760897	NONHSAT124971
6	lnc-RP1L1-5	chr8:9758941-9760901	NONHSAT124972

Variant related genes	Relation type
LINC00599	TF binding region

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11987861	0.88[EUR][1000 genomes]
rs12056944	0.82[EUR][1000 genomes]
rs12543685	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12543996	0.84[EUR][1000 genomes]
rs12544019	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12545481	0.87[EUR][1000 genomes]
rs12548011	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12549629	0.87[EUR][1000 genomes]
rs13252210	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13270146	0.82[EUR][1000 genomes]
rs1708879	0.82[YRI][hapmap]
rs17150693	0.85[EUR][1000 genomes]
rs1962430	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2055729	0.86[CEU][hapmap]
rs4841254	0.88[CEU][hapmap]
rs491364	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs506276	0.90[CEU][hapmap]
rs531564	1.00[ASW][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs59880252	0.80[EUR][1000 genomes]
rs612689	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62489486	0.89[EUR][1000 genomes]
rs62489489	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6981023	0.82[ASN][1000 genomes]
rs6989793	0.81[EUR][1000 genomes]
rs6996932	0.87[EUR][1000 genomes]
rs7828229	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs592420	MFHAS1	cis	cerebellum	SCAN
rs592420	PRSS55	cis	cerebellum	SCAN
rs592420	PPP1R3B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9757800-9761000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
2	chr8:9758000-9761600	Active TSS	Brain Angular Gyrus	brain
3	chr8:9759600-9760600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:9759600-9761200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:9759600-9764000	Active TSS	Fetal Brain Male	brain
6	chr8:9759800-9760600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
7	chr8:9759800-9760800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
8	chr8:9759800-9761000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr8:9760000-9760600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:9760000-9760600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:9760000-9760600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:9760000-9760600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
13	chr8:9760000-9760600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr8:9760000-9760600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:9760000-9760600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
16	chr8:9760000-9760600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr8:9760000-9760600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
18	chr8:9760000-9760800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr8:9760000-9760800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
20	chr8:9760000-9761200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
21	chr8:9760000-9762800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr8:9760200-9760600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr8:9760200-9760600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr8:9760200-9760600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
25	chr8:9760200-9760600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr8:9760200-9760600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr8:9760200-9760600	Bivalent Enhancer	Fetal Lung	lung
28	chr8:9760200-9760600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
29	chr8:9760200-9760800	Enhancers	Gastric	stomach
30	chr8:9760200-9761000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr8:9760200-9761200	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
32	chr8:9760200-9761800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr8:9760200-9762600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:9760200-9765000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr8:9760200-9765400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr8:9760200-9765800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr8:9760400-9760600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
38	chr8:9760400-9760600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
39	chr8:9760400-9760600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr8:9760400-9760600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
41	chr8:9760400-9760600	Bivalent/Poised TSS	Brain Substantia Nigra	brain
42	chr8:9760400-9760600	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr8:9760400-9760600	Bivalent Enhancer	Fetal Kidney	kidney
44	chr8:9760400-9761000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr8:9760400-9761200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr8:9760400-9762200	Active TSS	H1 Cell Line	embryonic stem cell
47	chr8:9760400-9762400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
48	chr8:9760400-9764600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr8:9760400-9764600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
50	chr8:9760400-9764800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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