Variant report

Variant	rs6743542
Chromosome Location	chr2:31355047-31355048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BACH1	chr2:31354877-31355053	H1-hESC	embryonic stem cell:	n/a	n/a
2	EBF1	chr2:31354961-31355283	GM12878	blood:	n/a	n/a
3	JUND	chr2:31354876-31355064	H1-hESC	embryonic stem cell:	n/a	chr2:31355036-31355046

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:31354945..31357543-chr2:31362533..31364152,2	MCF-7	breast:

Variant related genes	Relation type
GALNT14	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10190164	1.00[JPT][hapmap]
rs10201005	1.00[JPT][hapmap]
rs11675787	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11684970	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12989636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17010764	0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs2008535	0.90[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59588353	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60245472	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6543605	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543606	0.90[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6543607	1.00[JPT][hapmap]
rs6543609	0.94[JPT][hapmap]
rs6706156	1.00[JPT][hapmap]
rs6747497	1.00[CEU][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7560152	0.86[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7560583	0.96[ASN][1000 genomes]
rs7596724	0.80[CEU][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs956747	0.81[CEU][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]

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
rs6743542	SRD5A2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31347800-31358800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:31349600-31355600	Weak transcription	HMEC	breast
3	chr2:31349800-31355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:31349800-31357200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:31350000-31355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:31350000-31359600	Weak transcription	Pancreas	Pancrea
7	chr2:31350200-31355800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:31351600-31358600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:31351600-31359600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:31351800-31355400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:31352400-31356000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr2:31352600-31355600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr2:31353000-31356000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:31353200-31355200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:31353400-31358600	Enhancers	Brain Germinal Matrix	brain
16	chr2:31353400-31359600	Weak transcription	Spleen	Spleen
17	chr2:31354000-31355600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:31354000-31355800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr2:31354200-31355600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr2:31354200-31355800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr2:31354200-31356000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:31354400-31355200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:31354400-31355600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr2:31354400-31355600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:31354400-31356800	Enhancers	NHEK	skin
26	chr2:31354600-31356800	Weak transcription	Fetal Brain Male	brain
27	chr2:31355000-31355600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr2:31355000-31355800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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