Variant report

Variant	rs4851250
Chromosome Location	chr2:100729293-100729294
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	chr2:100729149..100730802-chr2:100730864..100732886,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10192951	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10209201	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10211595	0.81[CHB][hapmap]
rs11682173	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs12996621	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13001130	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13001783	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13011181	0.86[AFR][1000 genomes]
rs13020141	0.87[AMR][1000 genomes]
rs13022707	0.86[AFR][1000 genomes]
rs13033732	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13402289	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13402299	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13430705	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17023468	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1821830	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2118281	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34040706	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34714421	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35300735	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35730185	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35774174	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35840153	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35869550	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4851243	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851244	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4851254	0.85[CEU][hapmap]
rs56037757	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56935201	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58683655	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59447631	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60311127	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60697219	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71413861	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7572939	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7596359	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9784000	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv458707	chr2:100687778-100753490	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv582529	chr2:100687778-100753490	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4851250	SNRNP200	cis	parietal	SCAN
rs4851250	MGAT4A	cis	parietal	SCAN
rs4851250	AFF3	cis	parietal	SCAN
rs4851250	C2orf64	cis	cerebellum	SCAN
rs4851250	AFF3	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100722000-100729400	Weak transcription	Dnd41	blood
2	chr2:100722400-100730000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:100726800-100730000	Weak transcription	Spleen	Spleen
4	chr2:100726800-100730400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:100727200-100729400	Weak transcription	Thymus	Thymus
6	chr2:100727200-100730600	Genic enhancers	Primary B cells from peripheral blood	blood
7	chr2:100727600-100729600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:100727600-100730600	Enhancers	Primary T cells from cord blood	blood
9	chr2:100727800-100729600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:100727800-100729800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:100727800-100729800	Genic enhancers	Primary B cells from cord blood	blood
12	chr2:100727800-100730000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:100728400-100729800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:100728600-100731800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr2:100728800-100729400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:100728800-100732000	Enhancers	Fetal Thymus	thymus
17	chr2:100729200-100731800	Enhancers	Primary T helper cells PMA-I stimulated	--

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