Variant report

Variant	rs2938325
Chromosome Location	chr1:114588338-114588339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114555472..114558426-chr1:114586301..114588819,2	MCF-7	breast:
2	chr1:114587184..114588685-chr1:114594720..114597075,2	MCF-7	breast:
3	chr1:114585196..114589086-chr1:114619214..114622779,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10776776	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776777	1.00[ASN][1000 genomes]
rs10858028	0.85[EUR][1000 genomes]
rs11102721	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330700	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1394075	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1587773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604781	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1910486	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938317	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938324	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938334	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938336	1.00[ASN][1000 genomes]
rs2938337	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938338	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938339	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938340	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs2938341	1.00[ASN][1000 genomes]
rs2938342	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938343	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2938344	1.00[ASN][1000 genomes]
rs2938345	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938349	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938350	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938351	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938353	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3006985	0.88[ASN][1000 genomes]
rs3006986	0.88[ASN][1000 genomes]
rs3006991	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006992	1.00[ASN][1000 genomes]
rs3006993	0.93[ASN][1000 genomes]
rs3006994	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006995	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3006997	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007004	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007005	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007007	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007010	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3007012	0.92[EUR][1000 genomes]
rs3007013	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240537	0.86[EUR][1000 genomes]
rs514647	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs529171	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs548040	0.91[EUR][1000 genomes];0.83[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2754686	chr1:114531958-114602958	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv463284	chr1:114585590-114623867	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv547568	chr1:114585590-114623867	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv547569	chr1:114587766-114625425	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2938325	DENND2C	cis	parietal	SCAN
rs2938325	CSDE1	cis	cerebellum	SCAN
rs2938325	FAM46C	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114583000-114590400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:114583800-114590200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:114584800-114590600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr1:114585800-114590400	Weak transcription	Spleen	Spleen

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