Variant report

Variant	rs11679835
Chromosome Location	chr2:172226754-172226755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172226142..172229101-chr2:172289900..172293776,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123600	Chromatin interaction
ENSG00000115827	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10454741	0.82[EUR][1000 genomes]
rs11674632	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11677795	0.88[EUR][1000 genomes]
rs11687454	0.84[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs11691073	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs11694321	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11893310	0.86[EUR][1000 genomes]
rs11902733	0.88[EUR][1000 genomes]
rs12105780	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12989392	0.84[EUR][1000 genomes]
rs12989938	0.84[EUR][1000 genomes]
rs12998320	1.00[GIH][hapmap]
rs13000846	0.90[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs13002817	0.85[EUR][1000 genomes]
rs13003130	0.85[EUR][1000 genomes]
rs13005615	0.93[EUR][1000 genomes]
rs13023287	0.80[EUR][1000 genomes]
rs13023417	0.83[EUR][1000 genomes]
rs13023973	0.85[CEU][hapmap];0.96[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs13031794	0.85[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs13398989	0.90[EUR][1000 genomes]
rs2111459	0.85[CEU][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs2356707	0.81[EUR][1000 genomes]
rs34787101	0.87[EUR][1000 genomes]
rs36140780	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67077741	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6722670	0.90[CEU][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs7592018	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11679835	CYBRD1	cis	cerebellum	SCAN
rs11679835	CDCA7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172211000-172242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172212400-172231400	Weak transcription	Esophagus	oesophagus
3	chr2:172214800-172231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:172215400-172231800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:172215800-172231000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:172216400-172231400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:172217200-172231400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:172222200-172289600	Weak transcription	Gastric	stomach
9	chr2:172222400-172240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:172222800-172230400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:172223000-172235400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:172223000-172242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:172224200-172228000	Weak transcription	Right Atrium	heart
14	chr2:172225800-172231600	Weak transcription	Liver	Liver

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