Variant report

Variant	rs1248860
Chromosome Location	chr3:85015779-85015780
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	chr3:85011548..85014009-chr3:85014905..85018347,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1016305	0.80[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs1016306	0.80[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1248857	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1248858	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1248859	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs13081745	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1694977	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1872553	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1872556	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2035561	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2035562	0.90[CHB][hapmap]
rs2326123	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs4301023	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4499618	0.81[CHB][hapmap]
rs7651996	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs765461	0.85[CHB][hapmap]
rs9816652	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9831123	0.81[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834688	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840607	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1248860	CADM2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85011200-85016600	Weak transcription	Psoas Muscle	Psoas
2	chr3:85011200-85016800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:85011200-85016800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:85011600-85016800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:85011600-85016800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:85011600-85018400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr3:85012000-85016800	Weak transcription	Brain Germinal Matrix	brain
8	chr3:85013400-85019200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:85013600-85016800	Weak transcription	Fetal Brain Female	brain
10	chr3:85013800-85016600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:85014200-85016200	Enhancers	Brain Substantia Nigra	brain
12	chr3:85014200-85016600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:85014400-85016600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:85014400-85016800	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:85014400-85020000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:85014600-85016800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:85014800-85016200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr3:85014800-85016600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:85014800-85016600	Enhancers	Brain Hippocampus Middle	brain
20	chr3:85014800-85016800	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:85015000-85016200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:85015200-85016200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:85015200-85016200	Enhancers	Brain Angular Gyrus	brain
24	chr3:85015200-85016400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:85015200-85016400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:85015200-85016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:85015200-85016800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:85015200-85016800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:85015400-85016000	Enhancers	Fetal Brain Male	brain
30	chr3:85015400-85016800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:85015400-85016800	Weak transcription	Brain Anterior Caudate	brain

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