Variant report

Variant	rs4974104
Chromosome Location	chr3:51383354-51383355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10433609	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs10865970	0.84[EUR][1000 genomes]
rs11130280	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs11130286	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs11130290	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs11706571	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs12632046	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12715446	0.80[ASN][1000 genomes]
rs1318649	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs1383251	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1480353	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]
rs1480354	0.84[EUR][1000 genomes]
rs1480360	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap];0.80[ASN][1000 genomes]
rs1480362	0.95[CHB][hapmap]
rs1480364	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs1542574	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]
rs1552074	0.92[CEU][hapmap]
rs17051762	0.91[CEU][hapmap]
rs1996331	0.80[ASN][1000 genomes]
rs2061950	0.95[CHB][hapmap];0.80[YRI][hapmap]
rs2101055	0.83[ASN][1000 genomes]
rs2127655	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs2164599	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2170178	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs2219890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[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];0.99[ASN][1000 genomes]
rs2219891	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs2241784	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2355943	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs2883809	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs2883812	0.83[ASN][1000 genomes]
rs3856932	0.90[CHB][hapmap]
rs4367100	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs4475072	0.90[CHB][hapmap]
rs4538365	0.80[ASN][1000 genomes]
rs4560329	0.86[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap]
rs4687800	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4927970	0.95[CHB][hapmap]
rs4974092	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs4974094	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs4974099	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs4974105	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974106	0.84[EUR][1000 genomes]
rs4974108	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs6445549	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs6445601	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs6445604	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs6445611	0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs6445620	1.00[CEU][hapmap]
rs6445622	1.00[CEU][hapmap]
rs6445628	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6445727	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6772668	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6774745	0.81[AMR][1000 genomes]
rs6784455	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs6787805	0.95[CHB][hapmap];0.83[CHD][hapmap];0.91[MEX][hapmap]
rs6796847	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs751075	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7614317	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs7616967	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7617533	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7625821	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7630714	0.83[ASN][1000 genomes]
rs7633708	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7634799	0.95[CHB][hapmap]
rs7640083	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs7648012	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649069	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.85[ASN][1000 genomes]
rs7651141	1.00[CHB][hapmap]
rs899750	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs9832672	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs9836464	0.80[ASN][1000 genomes]
rs9844581	0.95[CHB][hapmap]
rs9856566	1.00[CHB][hapmap]
rs9860403	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]
rs9870281	0.80[ASN][1000 genomes]
rs9877188	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs995543	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4974104	HYAL2	cis	parietal	SCAN
rs4974104	IQCF2	cis	parietal	SCAN
rs4974104	HEMK1	cis	cerebellum	SCAN
rs4974104	TEX264	cis	Nerve Tibial	GTEx
rs4974104	MST1	cis	cerebellum	SCAN
rs4974104	TEX264	cis	Esophagus Muscularis	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51369600-51383800	Weak transcription	Fetal Brain Male	brain
2	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:51378400-51389800	Weak transcription	Brain Substantia Nigra	brain
6	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:51378800-51383800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:51378800-51387400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:51378800-51388000	Weak transcription	Brain Angular Gyrus	brain
10	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
11	chr3:51379000-51386000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
15	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:51379400-51383800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
22	chr3:51381400-51392000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:51381800-51387400	Weak transcription	Fetal Brain Female	brain
24	chr3:51381800-51392200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:51382200-51387200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:51382400-51389800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr3:51382600-51386600	Weak transcription	NHEK	skin
28	chr3:51382800-51386200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr3:51382800-51386800	Weak transcription	HMEC	breast
30	chr3:51382800-51392200	Weak transcription	HSMMtube	muscle
31	chr3:51383000-51391000	Weak transcription	Brain Hippocampus Middle	brain

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