Variant report

Variant	rs1962430
Chromosome Location	chr8:9759620-9759621
allele	A/C
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	chr8:9758404-9764972	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr8:9759530-9764640	SK-N-SH	brain:	n/a	n/a
3	REST	chr8:9759431-9765302	H1-neurons	neurons:	n/a	chr8:9763658-9763671 chr8:9760877-9760897 chr8:9761543-9761556 chr8:9764262-9764271 chr8:9761633-9761646
4	POLR2A	chr8:9759593-9760064	HL-60	blood:	n/a	n/a

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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10098618	0.80[EUR][1000 genomes]
rs10104236	0.82[EUR][1000 genomes]
rs10108550	0.82[EUR][1000 genomes]
rs11987861	0.87[EUR][1000 genomes]
rs12056944	0.82[EUR][1000 genomes]
rs12543685	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12543996	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12544019	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12545481	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12546952	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12548011	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12549629	0.84[EUR][1000 genomes]
rs13252210	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13270146	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17150693	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs491364	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs592420	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59880252	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs612689	0.84[EUR][1000 genomes]
rs62489486	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62489489	0.86[EUR][1000 genomes]
rs6601389	0.82[EUR][1000 genomes]
rs6601390	0.81[EUR][1000 genomes]
rs6601393	0.82[EUR][1000 genomes]
rs6989793	0.80[EUR][1000 genomes]
rs6990268	0.82[EUR][1000 genomes]
rs6996932	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7828229	0.81[AMR][1000 genomes];0.87[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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9757200-9759800	Enhancers	H1 Cell Line	embryonic stem cell
2	chr8:9757400-9759800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
3	chr8:9757600-9760000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
4	chr8:9757800-9759800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
5	chr8:9757800-9759800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
6	chr8:9757800-9761000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
7	chr8:9758000-9760200	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr8:9758000-9761600	Active TSS	Brain Angular Gyrus	brain
9	chr8:9758200-9760200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:9758600-9759800	Active TSS	Brain Cingulate Gyrus	brain
11	chr8:9758600-9759800	Active TSS	Brain Hippocampus Middle	brain
12	chr8:9758600-9760000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr8:9758600-9760200	Active TSS	Brain Anterior Caudate	brain
14	chr8:9758800-9759800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
15	chr8:9758800-9759800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:9759000-9760000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr8:9759000-9760000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:9759200-9760400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
19	chr8:9759400-9759800	Enhancers	H9 Cell Line	embryonic stem cell
20	chr8:9759400-9759800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr8:9759600-9759800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr8:9759600-9759800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr8:9759600-9760400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:9759600-9760600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr8:9759600-9761200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:9759600-9764000	Active TSS	Fetal Brain Male	brain

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