Variant report

Variant	rs1484645
Chromosome Location	chr8:10000966-10000967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10107485	0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs11249969	0.82[CHB][hapmap]
rs1160369	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11774411	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11783851	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11785434	0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11785454	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11998591	0.86[CHD][hapmap]
rs12542030	0.82[ASN][1000 genomes]
rs12545469	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12545775	0.85[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12545788	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12545826	0.82[CHB][hapmap]
rs12547884	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12549943	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12550244	0.83[CHB][hapmap]
rs12674871	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12680389	0.87[CHB][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs13249013	0.91[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs13256357	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1466555	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1564808	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17151108	0.83[CHD][hapmap]
rs17151142	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17151145	0.81[CHD][hapmap]
rs17151147	0.81[CHD][hapmap]
rs17151190	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17151193	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs17151201	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17155393	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1984863	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1994223	0.83[CHD][hapmap]
rs2016221	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898242	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3735823	0.82[CHB][hapmap]
rs4294187	0.83[CHB][hapmap]
rs4840463	0.81[CHD][hapmap];0.85[JPT][hapmap]
rs4841279	0.87[CHB][hapmap]
rs4841283	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66602888	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6983566	0.82[CHB][hapmap]
rs6985791	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7008407	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7008695	0.84[ASN][1000 genomes]
rs7012601	0.89[ASN][1000 genomes]
rs7016690	0.89[ASN][1000 genomes]
rs72626643	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7830843	0.91[ASN][1000 genomes]
rs7843906	0.83[CHD][hapmap]
rs9329215	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9644681	0.83[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv890344	chr8:9995515-10060638	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1484645	CLDN23	cis	multi-tissue	Pritchard
rs1484645	C8orf48	cis	cerebellum	SCAN
rs1484645	FLJ10661	cis	cerebellum	SCAN
rs1484645	FAM167A	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9986200-10002200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:9988800-10002200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr8:9991200-10004600	Weak transcription	Esophagus	oesophagus
4	chr8:9992200-10004800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr8:9992200-10004800	Weak transcription	Right Ventricle	heart
6	chr8:9996400-10020200	Weak transcription	Pancreas	Pancrea
7	chr8:9996600-10004600	Weak transcription	Gastric	stomach
8	chr8:9996600-10004800	Weak transcription	Left Ventricle	heart
9	chr8:9996600-10005000	Weak transcription	Right Atrium	heart
10	chr8:9996600-10036200	Weak transcription	Primary T cells from cord blood	blood
11	chr8:9996800-10009600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr8:9997000-10010200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:9997200-10002600	Weak transcription	Liver	Liver
14	chr8:9998600-10001200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr8:10000000-10001400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:10000000-10003000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:10000200-10001400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr8:10000400-10001000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr8:10000400-10001400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr8:10000400-10002000	Flanking Active TSS	Fetal Brain Female	brain
21	chr8:10000400-10003200	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr8:10000600-10001000	Active TSS	Brain Cingulate Gyrus	brain
23	chr8:10000600-10001000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr8:10000600-10001400	Active TSS	Brain Angular Gyrus	brain
25	chr8:10000600-10001400	Active TSS	Brain Anterior Caudate	brain
26	chr8:10000600-10001400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr8:10000600-10001400	Active TSS	Brain Substantia Nigra	brain
28	chr8:10000600-10001400	Flanking Active TSS	NH-A	brain
29	chr8:10000600-10002600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr8:10000600-10002800	Enhancers	H1 Cell Line	embryonic stem cell
31	chr8:10000800-10001000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr8:10000800-10001000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr8:10000800-10001000	Active TSS	Brain Hippocampus Middle	brain
34	chr8:10000800-10001200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr8:10000800-10001200	Enhancers	Fetal Brain Male	brain
36	chr8:10000800-10001400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr8:10000800-10001600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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