Variant report

Variant	rs13083852
Chromosome Location	chr3:155139253-155139254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11706749	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11709568	0.86[CHD][hapmap]
rs11713552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715278	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11928089	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12487150	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12493778	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496803	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12631218	0.90[CHD][hapmap]
rs12696031	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs13066178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100169	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2351	0.88[CHD][hapmap]
rs2352	0.88[CHD][hapmap]
rs35424673	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345113	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4524323	0.81[ASN][1000 genomes]
rs4630984	0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs4679744	0.82[ASN][1000 genomes]
rs4679745	0.91[CHD][hapmap]
rs4680171	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4680172	0.96[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap]
rs4680173	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680174	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680175	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680176	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680178	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4680185	0.88[CHD][hapmap]
rs6440985	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440993	0.86[CHD][hapmap]
rs6440994	0.84[CHD][hapmap]
rs6440995	0.84[CHD][hapmap]
rs6762452	0.92[EUR][1000 genomes]
rs6794214	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs6802079	0.91[CHD][hapmap]
rs6807784	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6807961	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612603	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7615026	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs7618495	0.86[CHD][hapmap]
rs7619730	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627097	0.89[CEU][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823946	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs9829532	0.86[CHD][hapmap]
rs9841365	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9848852	0.88[CHD][hapmap]
rs9869956	0.93[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv877679	chr3:155128968-155204939	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13083852	BRD7	cis	parietal	SCAN
rs13083852	PLCH1	cis	parietal	SCAN
rs13083852	SLC33A1	cis	cerebellum	SCAN
rs13083852	GFM1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155136000-155141400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:155136400-155141200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:155136600-155141600	Weak transcription	Fetal Brain Male	brain
4	chr3:155136600-155141800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:155136600-155142400	Weak transcription	Fetal Brain Female	brain
6	chr3:155136800-155141800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:155137000-155141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:155138000-155141000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:155138400-155139800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:155138400-155140200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:155138400-155140200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr3:155138400-155140400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:155138400-155141000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:155138600-155139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:155138600-155140400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:155138600-155140600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:155138800-155139600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:155138800-155139600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:155138800-155139800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr3:155138800-155140000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr3:155138800-155140600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:155138800-155140600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:155139000-155139400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:155139000-155139600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:155139200-155139400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr3:155139200-155139600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:155139200-155141400	Weak transcription	Fetal Thymus	thymus
28	chr3:155139200-155141600	Weak transcription	Fetal Muscle Leg	muscle

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