Variant report

Variant	rs4974105
Chromosome Location	chr3:51369574-51369575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51367010..51371078-chr3:51375773..51379297,4	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10212250	0.86[CHB][hapmap]
rs1031925	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1055429	0.82[AMR][1000 genomes]
rs10865970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130282	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11130293	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11721253	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632046	0.84[EUR][1000 genomes]
rs1383251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1383252	1.00[CHB][hapmap]
rs1480353	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1480354	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480358	0.86[CHB][hapmap]
rs1480363	0.86[CHB][hapmap]
rs1542574	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]
rs1552072	0.86[CHB][hapmap]
rs1552073	0.86[CHB][hapmap]
rs1552074	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17051734	0.85[CHB][hapmap]
rs17051762	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs2061951	0.86[CHB][hapmap]
rs2127655	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2219890	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2241784	0.82[EUR][1000 genomes]
rs2355934	0.86[CHB][hapmap]
rs2355941	0.86[CHB][hapmap]
rs4244697	0.86[CHB][hapmap]
rs4301044	0.86[CHB][hapmap]
rs4328835	0.84[CHB][hapmap]
rs4367101	0.86[CHB][hapmap]
rs4378999	0.86[CHB][hapmap]
rs4428169	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4453876	0.86[CHB][hapmap]
rs4528983	0.86[CHB][hapmap]
rs4532165	0.86[CHB][hapmap]
rs4568177	0.86[CHB][hapmap]
rs4611808	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687569	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974095	0.86[CHB][hapmap]
rs4974104	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4974106	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974109	0.82[MEX][hapmap]
rs6445455	0.86[CHB][hapmap]
rs6445551	0.86[CHB][hapmap]
rs6445620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6445622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445624	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772664	0.86[CHB][hapmap]
rs6773260	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6777719	0.86[CHB][hapmap]
rs6779658	0.86[CHB][hapmap]
rs6793900	0.82[AMR][1000 genomes]
rs6809080	0.86[CHB][hapmap]
rs7372658	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7427006	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs751075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][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];0.97[ASN][1000 genomes]
rs7619584	0.85[CHB][hapmap]
rs7625006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628533	0.86[CHB][hapmap]
rs7633708	0.84[CEU][hapmap]
rs7644957	0.86[CHB][hapmap]
rs7648012	0.92[CEU][hapmap]
rs922612	0.86[CHB][hapmap]
rs9311469	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9855442	0.84[CHB][hapmap]
rs9858412	0.86[CHB][hapmap]
rs9869123	1.00[CHB][hapmap]
rs9871539	0.86[CHB][hapmap]
rs9878100	0.86[CHB][hapmap]
rs9883739	0.86[CHB][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4974105	MST1	cis	cerebellum	SCAN
rs4974105	PARP3	cis	parietal	SCAN
rs4974105	NCKIPSD	cis	cerebellum	SCAN
rs4974105	HYAL2	cis	parietal	SCAN
rs4974105	TEX264	cis	Nerve Tibial	GTEx
rs4974105	HEMK1	cis	cerebellum	SCAN
rs4974105	TEX264	cis	Esophagus Muscularis	GTEx
rs4974105	TEX264	cis	Artery Tibial	GTEx
rs4974105	IQCF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51340000-51370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:51341600-51372000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:51344200-51371800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:51352800-51369800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:51353000-51370000	Weak transcription	Brain Germinal Matrix	brain
6	chr3:51353000-51370200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:51353200-51370200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:51353400-51375800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:51353400-51377600	Weak transcription	Left Ventricle	heart
10	chr3:51358000-51376200	Weak transcription	HSMMtube	muscle
11	chr3:51358800-51377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:51364200-51375800	Weak transcription	Right Ventricle	heart
13	chr3:51366400-51377600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:51366600-51377400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:51366800-51371400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:51367200-51371600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:51367400-51372000	Strong transcription	Brain Angular Gyrus	brain
18	chr3:51367600-51377800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:51368000-51377400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:51368200-51369600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:51368200-51369800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:51369200-51371600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:51369200-51372000	Strong transcription	Brain Hippocampus Middle	brain
24	chr3:51369200-51374600	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr3:51369400-51372000	Strong transcription	Fetal Brain Female	brain
26	chr3:51369400-51377400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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