Variant report

Variant	rs12692886
Chromosome Location	chr2:169623949-169623950
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:169622048..169624666-chr2:169632656..169634335,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1063729	0.86[MEX][hapmap]
rs13017628	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1402840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855872	1.00[CHB][hapmap]
rs2390731	0.83[ASN][1000 genomes]
rs3845726	1.00[CHB][hapmap]
rs3845727	1.00[CHB][hapmap]
rs3856426	1.00[CHB][hapmap]
rs3914920	1.00[CHB][hapmap]
rs4233821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668101	0.83[ASN][1000 genomes]
rs4668103	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6433088	0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs6433092	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558965	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs7585751	0.83[ASN][1000 genomes]
rs7589456	0.83[ASN][1000 genomes]
rs8304	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9287901	0.86[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	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12692886	C2orf77	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169579600-169630200	Weak transcription	Aorta	Aorta
2	chr2:169579600-169630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:169586000-169627600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:169597200-169635800	Weak transcription	Ovary	ovary
5	chr2:169601600-169625800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:169604800-169627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:169606000-169630600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:169606000-169630600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:169606200-169630400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:169606600-169630600	Weak transcription	Gastric	stomach
11	chr2:169606600-169632800	Weak transcription	Pancreas	Pancrea
12	chr2:169608000-169625800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:169608200-169633800	Weak transcription	Psoas Muscle	Psoas
14	chr2:169608400-169626800	Weak transcription	Fetal Lung	lung
15	chr2:169608400-169627600	Weak transcription	HSMM	muscle
16	chr2:169608400-169632200	Weak transcription	HSMMtube	muscle
17	chr2:169608400-169633600	Weak transcription	Dnd41	blood
18	chr2:169609000-169628000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:169609200-169636400	Weak transcription	Lung	lung
20	chr2:169609400-169633000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:169609600-169634200	Weak transcription	Fetal Brain Male	brain
22	chr2:169610000-169625800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:169610000-169630600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:169610800-169637400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:169611200-169636600	Weak transcription	HepG2	liver
26	chr2:169611600-169625800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:169611600-169626800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:169612600-169625800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:169614000-169625800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:169614200-169628000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:169614400-169625600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:169614400-169631800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:169615800-169625800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr2:169615800-169626600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:169615800-169630600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:169616000-169625800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:169618000-169628200	Weak transcription	Brain Angular Gyrus	brain
38	chr2:169618000-169630400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:169619600-169630400	Weak transcription	HUVEC	blood vessel
40	chr2:169620000-169628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:169620200-169624400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:169620200-169626600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:169620600-169624600	Strong transcription	Primary T cells from cord blood	blood
44	chr2:169620800-169626400	Strong transcription	GM12878-XiMat	blood
45	chr2:169621200-169627000	Weak transcription	Fetal Kidney	kidney
46	chr2:169621400-169626600	Strong transcription	Brain Germinal Matrix	brain
47	chr2:169621400-169630400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:169621600-169624400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:169621600-169631000	Strong transcription	Fetal Thymus	thymus
50	chr2:169622000-169624400	Enhancers	Breast Myoepithelial Primary Cells	Breast

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