Variant report

Variant	rs742048
Chromosome Location	chr1:166910145-166910146
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:166902983..166904959-chr1:166908217..166910309,2	K562	blood:
2	chr1:166907906..166910353-chr1:166911637..166913490,2	K562	blood:
3	chr1:166900056..166902619-chr1:166907866..166910661,3	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10800276	0.88[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs10918599	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918600	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10918603	0.82[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10918607	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs11576904	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11578336	0.95[GIH][hapmap]
rs11579987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588176	0.97[ASN][1000 genomes]
rs12562794	0.80[TSI][hapmap]
rs12569084	0.95[GIH][hapmap]
rs2038020	0.91[ASN][1000 genomes]
rs2038022	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2072742	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2142615	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2235184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2280995	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs2294220	0.98[ASN][1000 genomes]
rs2312675	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4657613	0.88[CEU][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs61815130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815132	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427047	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427048	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6660048	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs6677644	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6695162	0.95[GIH][hapmap]
rs6695609	0.88[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs6699159	0.95[GIH][hapmap]
rs7518155	0.95[GIH][hapmap]
rs7520897	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7528849	0.95[GIH][hapmap]
rs7533688	0.95[GIH][hapmap]
rs7545806	0.82[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7545911	0.95[GIH][hapmap]

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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs742048	RGS4	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166891000-166916400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:166892000-166913800	Weak transcription	Thymus	Thymus
3	chr1:166896400-166910400	Weak transcription	Left Ventricle	heart
4	chr1:166899600-166913000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:166900800-166913600	Weak transcription	GM12878-XiMat	blood
6	chr1:166904200-166913000	Weak transcription	HSMMtube	muscle
7	chr1:166904400-166913400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:166905800-166913600	Weak transcription	Right Atrium	heart
9	chr1:166905800-166915200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:166906000-166910600	Enhancers	Fetal Heart	heart
11	chr1:166906000-166910800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:166906000-166912800	Weak transcription	Dnd41	blood
13	chr1:166906000-166913000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:166906000-166913000	Weak transcription	Primary T cells from cord blood	blood
15	chr1:166907600-166914000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:166907800-166913800	Weak transcription	Brain Angular Gyrus	brain
17	chr1:166908600-166912800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:166909000-166913400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:166909000-166914000	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:166909000-166914000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:166909000-166914000	Weak transcription	Brain Substantia Nigra	brain
22	chr1:166909400-166910400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:166909600-166913000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:166909800-166913800	Weak transcription	Fetal Brain Male	brain
25	chr1:166910000-166912800	Weak transcription	HSMM	muscle

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