Variant report

Variant	rs915404
Chromosome Location	chr1:76602662-76602663
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1631357	1.00[CHD][hapmap]
rs167050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172334	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs190861	0.93[TSI][hapmap]
rs289678	0.88[TSI][hapmap]
rs289682	1.00[JPT][hapmap]
rs289683	1.00[JPT][hapmap]
rs289692	0.93[TSI][hapmap]
rs289698	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs289699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs289700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs289701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992502	1.00[JPT][hapmap]
rs2992503	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011995	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384233	0.85[EUR][1000 genomes]
rs387214	1.00[JPT][hapmap]
rs389899	1.00[JPT][hapmap]
rs399529	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403449	0.85[EUR][1000 genomes]
rs409245	0.85[EUR][1000 genomes]
rs418644	1.00[JPT][hapmap]
rs423152	1.00[JPT][hapmap]
rs447383	1.00[CHD][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs491409	0.83[EUR][1000 genomes]
rs551954	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs552890	0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs597362	1.00[JPT][hapmap]
rs61558985	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs622212	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs643289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs681280	1.00[JPT][hapmap]
rs860154	1.00[JPT][hapmap]
rs915402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs915403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1488	chr1:76587622-76632635	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs915404	LHX8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76557400-76605800	Weak transcription	Fetal Intestine Small	intestine
2	chr1:76575400-76606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:76576600-76620000	Weak transcription	Primary B cells from cord blood	blood
4	chr1:76587800-76602800	Weak transcription	Right Atrium	heart
5	chr1:76588200-76615600	Weak transcription	Left Ventricle	heart
6	chr1:76591200-76607800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:76592600-76610800	Weak transcription	Fetal Kidney	kidney
8	chr1:76592800-76605800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:76593000-76608200	Weak transcription	Fetal Lung	lung
10	chr1:76594200-76607400	Weak transcription	Fetal Brain Female	brain
11	chr1:76594600-76615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:76598600-76609800	Weak transcription	Fetal Stomach	stomach
13	chr1:76599800-76620200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:76601200-76603000	Enhancers	Brain Angular Gyrus	brain
15	chr1:76601200-76603000	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:76601200-76603400	Weak transcription	Psoas Muscle	Psoas
17	chr1:76601200-76604600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:76601400-76603800	Enhancers	Brain Anterior Caudate	brain
19	chr1:76601400-76604000	Enhancers	Brain Substantia Nigra	brain
20	chr1:76601600-76603600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:76601600-76605200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:76601800-76605600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:76601800-76606000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:76601800-76608200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:76602000-76607600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:76602400-76603200	Enhancers	Primary B cells from peripheral blood	blood

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