Variant report

Variant	rs2131730
Chromosome Location	chr15:57839788-57839789
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	chr15:57837700..57840998-chr15:57842272..57845131,4	MCF-7	breast:
2	chr15:57838697..57840945-chr15:57847167..57849747,2	K562	blood:

Variant related genes	Relation type
ENSG00000240874	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11856	0.90[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11856674	0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs12439291	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439292	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439665	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12439793	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs1626448	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1630903	0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1666572	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1666573	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1690316	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1690317	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1690318	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17820431	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820437	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17820449	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17820461	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17820467	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1908191	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1908192	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2131731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131733	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2270487	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2270488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2279606	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs2635389	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2922231	0.85[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2922232	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2932208	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2932209	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2934418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742963	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742964	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774962	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55916627	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55952634	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56362917	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59368768	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66802357	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67336499	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166305	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171354	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171360	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72741522	0.94[ASN][1000 genomes]
rs72741528	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025786	0.92[ASN][1000 genomes]
rs8038795	0.90[CEU][hapmap];0.83[CHD][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs937248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv904255	chr15:57790436-57907574	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv976938	chr15:57838920-57842883	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2131730	RNF111	cis	cerebellum	SCAN
rs2131730	CCNB2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:57803200-57842800	Weak transcription	Aorta	Aorta
3	chr15:57819200-57841000	Weak transcription	Esophagus	oesophagus
4	chr15:57819800-57840000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:57821800-57842800	Strong transcription	Liver	Liver
6	chr15:57827600-57840600	Weak transcription	Fetal Lung	lung
7	chr15:57829400-57841200	Weak transcription	Left Ventricle	heart
8	chr15:57829400-57842600	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:57829600-57842000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:57829600-57843200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:57830000-57840800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:57830000-57846400	Weak transcription	Brain Substantia Nigra	brain
13	chr15:57830200-57842200	Strong transcription	Fetal Stomach	stomach
14	chr15:57830400-57843400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:57830600-57842200	Weak transcription	Brain Anterior Caudate	brain
16	chr15:57830800-57842400	Weak transcription	HUVEC	blood vessel
17	chr15:57831000-57839800	Weak transcription	Fetal Intestine Large	intestine
18	chr15:57831000-57840800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:57831400-57843400	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:57832400-57842600	Weak transcription	Fetal Kidney	kidney
21	chr15:57832400-57843200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:57833000-57841000	Weak transcription	Spleen	Spleen
23	chr15:57833400-57841400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:57834000-57843000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:57834800-57840000	Strong transcription	Placenta	Placenta
26	chr15:57834800-57843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:57835000-57839800	Weak transcription	Stomach Mucosa	stomach
28	chr15:57835200-57841800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr15:57835400-57843000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:57835800-57839800	Strong transcription	Gastric	stomach
31	chr15:57835800-57840000	Strong transcription	Ovary	ovary
32	chr15:57835800-57840200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:57835800-57840400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:57835800-57843200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:57836000-57839800	Strong transcription	Lung	lung
36	chr15:57836000-57840000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:57836200-57839800	Strong transcription	Pancreas	Pancrea
38	chr15:57836200-57840600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr15:57836200-57842000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:57836200-57843400	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr15:57836600-57839800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:57836600-57842200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:57837000-57839800	Strong transcription	Fetal Intestine Small	intestine
44	chr15:57837600-57841200	Weak transcription	Right Ventricle	heart
45	chr15:57837800-57840200	Strong transcription	HepG2	liver
46	chr15:57837800-57853000	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:57838600-57840000	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:57838800-57841200	Enhancers	Fetal Heart	heart
49	chr15:57839000-57840000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:57839200-57840000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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