Variant report

Variant	rs10516851
Chromosome Location	chr4:90837944-90837945
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	chr4:90831900..90833818-chr4:90835603..90838018,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10433954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10433955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10516853	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11722543	0.86[ASN][1000 genomes]
rs12640573	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs12640925	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12640973	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12641781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643823	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12644375	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12646270	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1372511	0.87[ASN][1000 genomes]
rs1372512	0.87[ASN][1000 genomes]
rs1442131	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1442132	0.81[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs16996201	0.91[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs17016274	0.88[JPT][hapmap]
rs17016373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17016396	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2241884	0.98[ASN][1000 genomes]
rs3775464	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3775465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775466	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3775467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3775473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775474	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775476	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3775477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775478	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56146644	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57925841	0.87[ASN][1000 genomes]
rs58514521	0.98[ASN][1000 genomes]
rs58930449	0.94[ASN][1000 genomes]
rs59345481	0.92[EUR][1000 genomes]
rs59559279	0.85[ASN][1000 genomes]
rs60847430	0.98[ASN][1000 genomes]
rs60909103	0.93[EUR][1000 genomes]
rs61160271	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs61611959	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6532197	0.81[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6532199	0.87[ASN][1000 genomes]
rs6532200	0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs67212195	0.84[ASN][1000 genomes]
rs6828095	0.87[ASN][1000 genomes]
rs6838943	0.97[ASN][1000 genomes]
rs6847403	0.87[ASN][1000 genomes]
rs6848022	0.87[ASN][1000 genomes]
rs6857668	0.93[ASN][1000 genomes]
rs6858182	0.95[ASN][1000 genomes]
rs72657800	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72657801	0.98[ASN][1000 genomes]
rs72657802	0.98[ASN][1000 genomes]
rs72659403	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72659404	0.98[ASN][1000 genomes]
rs72659409	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72659413	0.94[ASN][1000 genomes]
rs73831836	0.87[ASN][1000 genomes]
rs73831856	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7657014	0.81[ASN][1000 genomes]
rs7666981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673735	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv997700	chr4:90791866-90920021	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv830005	chr4:90799398-90963420	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1003903	chr4:90831805-90947922	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10516851	SLC10A6	cis	parietal	SCAN
rs10516851	MMRN1	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90828600-90841200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:90828800-90844200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:90830400-90838800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr4:90832000-90850400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:90832200-90846800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:90834800-90839000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:90837200-90838200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:90837400-90838000	Weak transcription	Brain Germinal Matrix	brain
9	chr4:90837400-90841200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr4:90837400-90841400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:90837600-90838000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:90837600-90838000	Weak transcription	Fetal Brain Male	brain
13	chr4:90837600-90841200	Weak transcription	HUVEC	blood vessel

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