Variant report

Variant	rs2634535
Chromosome Location	chr3:111034149-111034150
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111029720..111031793-chr3:111033589..111035195,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1352502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387225	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698347	1.00[ASN][1000 genomes]
rs2698354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2698355	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932040	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932041	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2950975	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2958081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2958084	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2971351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2971352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648997	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs979870	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997029	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2634535	ERP27	trans	parietal	SCAN
rs2634535	DPPA4	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111028600-111034200	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:111028800-111034200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:111028800-111034200	Enhancers	Fetal Thymus	thymus
4	chr3:111029000-111034400	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:111029000-111034400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:111029200-111034200	Enhancers	Primary T cells from cord blood	blood
7	chr3:111029400-111034200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:111029400-111034200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:111029400-111034200	Enhancers	Thymus	Thymus
10	chr3:111029800-111035200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:111031000-111034600	Weak transcription	Small Intestine	intestine
12	chr3:111031200-111034200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:111031200-111041800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:111031400-111042600	Enhancers	Dnd41	blood
15	chr3:111032800-111035400	Enhancers	HSMMtube	muscle
16	chr3:111033000-111034200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:111033000-111034200	Enhancers	Stomach Mucosa	stomach
18	chr3:111033000-111034400	Enhancers	Fetal Muscle Leg	muscle
19	chr3:111033000-111035200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:111033000-111035400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:111033200-111034200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:111033200-111034200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:111033200-111034800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:111033200-111035200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:111033200-111035200	Enhancers	NH-A	brain
26	chr3:111033200-111035600	Enhancers	HSMM	muscle
27	chr3:111033200-111042000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:111033400-111035200	Enhancers	Fetal Stomach	stomach
29	chr3:111033400-111035600	Enhancers	Fetal Lung	lung
30	chr3:111033600-111035400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:111033600-111040800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr3:111033600-111044200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:111033800-111035200	Enhancers	Fetal Intestine Small	intestine
34	chr3:111033800-111035400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:111033800-111035600	Enhancers	Hela-S3	cervix
36	chr3:111034000-111042400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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