Variant report

Variant	rs2365195
Chromosome Location	chr2:31312461-31312462
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	chr2:31310471..31312689-chr2:31376572..31378338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158089	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10490518	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10490519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865087	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11124238	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11124241	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1122261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11888670	0.80[MEX][hapmap]
rs12463945	0.88[CEU][hapmap]
rs12466133	0.82[EUR][1000 genomes]
rs12471972	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12993947	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12994752	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs13003016	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs13006348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13021484	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs13023792	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs13035341	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1862976	0.88[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs1991105	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2113490	0.92[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2194464	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2194465	0.88[EUR][1000 genomes]
rs2194470	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2194471	0.83[EUR][1000 genomes]
rs2216829	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2365193	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs2365204	0.85[EUR][1000 genomes]
rs2886303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3919588	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4337517	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4630806	0.81[CEU][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6543601	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs6708428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6748774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs749709	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs749710	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs749711	0.88[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs7565904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7592634	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs880618	0.92[CEU][hapmap];0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2365195	GALNT14	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31297400-31316400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:31302000-31321400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:31302600-31325200	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:31305400-31314000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:31307400-31331600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:31310600-31320800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:31310600-31346800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:31311000-31313200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:31311400-31313000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:31311600-31314800	Enhancers	NHEK	skin
11	chr2:31311800-31312800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:31312000-31313000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:31312200-31313400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:31312200-31314600	Weak transcription	HMEC	breast

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