Variant report

Variant	rs1542574
Chromosome Location	chr3:51395571-51395572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10212250	0.86[JPT][hapmap]
rs1031925	1.00[CEU][hapmap];0.83[CHD][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10865970	0.85[EUR][1000 genomes]
rs11130282	1.00[JPT][hapmap]
rs11130293	0.90[ASN][1000 genomes]
rs11721253	0.90[ASN][1000 genomes]
rs12632046	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1383251	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1383252	0.84[JPT][hapmap]
rs1480353	1.00[CEU][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1480354	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1480357	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs1480358	0.86[JPT][hapmap]
rs1480363	0.86[JPT][hapmap]
rs1552072	0.86[JPT][hapmap]
rs1552073	0.86[JPT][hapmap]
rs1552074	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051734	0.85[JPT][hapmap]
rs17051762	0.91[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2061951	0.86[JPT][hapmap]
rs2127655	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164599	0.81[EUR][1000 genomes]
rs2219890	1.00[CEU][hapmap];0.80[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2241784	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2355934	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2355941	0.86[JPT][hapmap]
rs4244697	0.86[JPT][hapmap]
rs4301044	0.86[JPT][hapmap]
rs4367101	0.86[JPT][hapmap]
rs4378999	0.86[JPT][hapmap]
rs4453876	0.86[JPT][hapmap]
rs4528983	0.85[JPT][hapmap]
rs4568177	0.86[JPT][hapmap]
rs4611808	0.95[ASN][1000 genomes]
rs4687569	0.95[ASN][1000 genomes]
rs4687800	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4974095	0.86[JPT][hapmap]
rs4974104	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4974105	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974106	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4974109	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs6445455	0.86[JPT][hapmap]
rs6445551	0.86[JPT][hapmap]
rs6445620	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs6445622	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6445628	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445727	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6772664	0.86[JPT][hapmap]
rs6772668	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6773260	0.85[ASN][1000 genomes]
rs6777719	0.86[JPT][hapmap]
rs6779658	0.86[JPT][hapmap]
rs6809080	0.86[JPT][hapmap]
rs7372658	0.83[ASN][1000 genomes]
rs751075	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7617533	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7619584	0.86[JPT][hapmap]
rs7625006	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7625821	0.80[EUR][1000 genomes]
rs7628533	0.86[JPT][hapmap]
rs7633708	0.84[CEU][hapmap];0.83[GIH][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7644957	0.86[JPT][hapmap]
rs7648012	0.92[CEU][hapmap];0.89[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs922612	0.86[JPT][hapmap]
rs9311469	0.90[ASN][1000 genomes]
rs9855442	0.86[JPT][hapmap]
rs9858412	0.86[JPT][hapmap]
rs9869123	0.85[CHB][hapmap]
rs9878100	0.86[JPT][hapmap]
rs9883739	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv460534	chr3:51393046-51416108	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv590274	chr3:51393046-51416108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv460535	chr3:51395571-51416108	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv590275	chr3:51395571-51416108	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1542574	HYAL2	cis	parietal	SCAN
rs1542574	MST1	cis	cerebellum	SCAN
rs1542574	HEMK1	cis	cerebellum	SCAN
rs1542574	TEX264	cis	Esophagus Muscularis	GTEx
rs1542574	IQCF2	cis	parietal	SCAN
rs1542574	TEX264	cis	Artery Tibial	GTEx
rs1542574	TEX264	cis	Nerve Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
4	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
5	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
9	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
10	chr3:51385400-51405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:51386400-51405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:51388400-51400800	Strong transcription	Brain Angular Gyrus	brain
13	chr3:51390200-51400400	Strong transcription	Fetal Brain Female	brain
14	chr3:51391000-51396600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:51391600-51406800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:51391800-51396600	Strong transcription	Stomach Smooth Muscle	stomach
17	chr3:51391800-51400400	Strong transcription	Brain Germinal Matrix	brain
18	chr3:51392000-51400600	Strong transcription	Brain Anterior Caudate	brain
19	chr3:51392600-51395800	Strong transcription	Brain Substantia Nigra	brain
20	chr3:51392800-51395800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:51392800-51400800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:51392800-51418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:51393000-51396400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:51393000-51400800	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr3:51393200-51405600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:51393600-51401000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:51393800-51398600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:51393800-51400800	Strong transcription	Brain Hippocampus Middle	brain
29	chr3:51394000-51405400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:51394400-51400800	Strong transcription	Brain Cingulate Gyrus	brain
31	chr3:51394400-51400800	Strong transcription	HSMMtube	muscle
32	chr3:51394600-51405400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:51395000-51399400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:51395200-51398000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:51395400-51395800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:51395400-51396000	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:51395400-51396000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:51395400-51397000	Weak transcription	Gastric	stomach
39	chr3:51395400-51400400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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