Variant report

Variant	rs2279606
Chromosome Location	chr15:57824386-57824387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57817814..57821842-chr15:57824294..57827570,5	K562	blood:
2	chr15:57817814..57819834-chr15:57824294..57826002,2	K562	blood:

Variant related genes	Relation type
ENSG00000261265	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11856674	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12439291	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs12439292	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[ASN][1000 genomes]
rs12439665	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12439793	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1620402	0.81[CHD][hapmap]
rs1623697	0.81[CHD][hapmap]
rs1666573	0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820431	1.00[ASW][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820437	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs17820449	0.88[ASN][1000 genomes]
rs17820461	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17820467	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2131730	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]
rs2131731	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs2270488	0.81[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2934418	0.90[ASN][1000 genomes]
rs3742963	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs3742964	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4774961	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4774962	0.92[ASN][1000 genomes]
rs55777040	1.00[AFR][1000 genomes]
rs55916627	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55952634	0.92[ASN][1000 genomes]
rs56362917	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59368768	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66802357	0.82[ASN][1000 genomes]
rs67336499	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166305	0.92[ASN][1000 genomes]
rs7171354	0.81[ASN][1000 genomes]
rs7171360	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72741522	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs72741528	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8025786	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs937248	0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.90[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	nsv833022	chr15:57657412-57830112	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279606	CCNB2	cis	parietal	SCAN
rs2279606	TMOD3	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57797000-57827200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:57802600-57846600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:57803200-57842800	Weak transcription	Aorta	Aorta
4	chr15:57811000-57827800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:57817000-57826600	Weak transcription	Lung	lung
6	chr15:57817200-57827800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:57819200-57841000	Weak transcription	Esophagus	oesophagus
8	chr15:57819800-57824800	Weak transcription	Fetal Kidney	kidney
9	chr15:57819800-57825200	Weak transcription	Left Ventricle	heart
10	chr15:57819800-57825200	Weak transcription	Right Atrium	heart
11	chr15:57819800-57826200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:57819800-57826400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr15:57819800-57829200	Weak transcription	Ovary	ovary
14	chr15:57819800-57833000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:57819800-57840000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:57820000-57825800	Weak transcription	Fetal Muscle Leg	muscle
17	chr15:57820000-57826600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:57820000-57826800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:57820200-57824600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:57820200-57825000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:57820200-57825400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:57820200-57825600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:57820200-57825800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:57820200-57829200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:57820200-57829400	Weak transcription	Brain Angular Gyrus	brain
26	chr15:57820600-57825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:57820600-57834000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:57820800-57825000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:57820800-57826200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:57821600-57824400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:57821600-57824800	Weak transcription	Placenta	Placenta
32	chr15:57821600-57825000	Weak transcription	Fetal Stomach	stomach
33	chr15:57821600-57825800	Weak transcription	Adipose Nuclei	Adipose
34	chr15:57821800-57842800	Strong transcription	Liver	Liver
35	chr15:57822000-57825600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:57822400-57829000	Weak transcription	Gastric	stomach
37	chr15:57822600-57824400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:57822600-57824600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:57822600-57824600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr15:57822600-57829200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr15:57822800-57824800	Weak transcription	Fetal Intestine Small	intestine
42	chr15:57822800-57826600	Weak transcription	HUVEC	blood vessel
43	chr15:57822800-57833000	Weak transcription	HepG2	liver
44	chr15:57822800-57834000	Weak transcription	Colon Smooth Muscle	Colon
45	chr15:57823000-57825000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:57823000-57827600	Enhancers	Fetal Heart	heart
47	chr15:57823000-57828800	Weak transcription	Pancreas	Pancrea
48	chr15:57823200-57825000	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:57823200-57825400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:57823400-57825200	Weak transcription	Brain Cingulate Gyrus	brain

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