Variant report

Variant	rs12639090
Chromosome Location	chr3:150114504-150114505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150108916..150110549-chr3:150112445..150115042,2	MCF-7	breast:
2	chr3:150103102..150105201-chr3:150113061..150115315,2	K562	blood:
3	chr3:150114227..150116746-chr3:150117310..150120155,2	MCF-7	breast:
4	chr3:150113690..150116562-chr3:150119441..150121130,4	K562	blood:
5	chr3:150109427..150111930-chr3:150114041..150117161,4	K562	blood:
6	chr3:150111999..150114822-chr3:150116151..150119153,3	K562	blood:
7	chr3:150111434..150116692-chr3:150125467..150130603,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10513373	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs10513374	0.85[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[ASN][1000 genomes]
rs10935800	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs11711035	0.96[ASN][1000 genomes]
rs11719654	0.86[YRI][hapmap]
rs11719977	0.94[ASN][1000 genomes]
rs12638309	0.98[ASN][1000 genomes]
rs13081231	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13099758	0.97[ASN][1000 genomes]
rs13321876	0.98[ASN][1000 genomes]
rs1450344	0.81[JPT][hapmap]
rs16862627	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs16862644	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs16862676	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1868672	0.90[JPT][hapmap]
rs1868673	0.81[JPT][hapmap]
rs2868425	0.81[JPT][hapmap]
rs34616287	0.89[AFR][1000 genomes]
rs35725711	0.90[AFR][1000 genomes]
rs4423794	0.85[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4681203	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681204	0.83[ASN][1000 genomes]
rs4681205	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4681206	0.96[ASN][1000 genomes]
rs4681207	0.83[ASN][1000 genomes]
rs4681616	0.83[ASN][1000 genomes]
rs4681617	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs4681618	0.85[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[ASN][1000 genomes]
rs58628422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67319423	0.98[ASN][1000 genomes]
rs6762432	0.91[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs6770424	0.91[JPT][hapmap]
rs6784048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6792734	0.96[ASN][1000 genomes]
rs6792759	0.81[JPT][hapmap]
rs6795124	0.94[ASN][1000 genomes]
rs6810143	0.91[JPT][hapmap]
rs73165707	0.83[ASN][1000 genomes]
rs7651989	0.81[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs9289810	0.91[JPT][hapmap]
rs9784335	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[ASN][1000 genomes]
rs9826729	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[ASN][1000 genomes]
rs9865031	0.96[ASN][1000 genomes]
rs9882777	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12639090	UBQLN4	cis	parietal	SCAN
rs12639090	TSC22D2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150090200-150124600	Weak transcription	Aorta	Aorta
2	chr3:150102800-150118200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:150109200-150124400	Weak transcription	HSMM	muscle
4	chr3:150109200-150124600	Weak transcription	NHLF	lung
5	chr3:150109400-150114600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:150109600-150114800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:150109600-150116800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:150109600-150121200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:150109800-150114600	Weak transcription	HUVEC	blood vessel
10	chr3:150112000-150116600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:150113200-150116800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:150113600-150114800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:150114200-150114600	Enhancers	Fetal Intestine Large	intestine
14	chr3:150114200-150114600	Enhancers	Fetal Intestine Small	intestine
15	chr3:150114200-150115200	Enhancers	Fetal Lung	lung
16	chr3:150114400-150114800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:150114400-150115400	Enhancers	Fetal Heart	heart

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