Variant report

Variant	rs3741621
Chromosome Location	chr12:49494025-49494026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49492241..49495096-chr12:49499639..49501320,2	MCF-7	breast:
2	chr12:49493937..49507579-chr12:49519161..49528577,46	K562	blood:
3	chr12:49493994..49495959-chr12:49498273..49500284,2	K562	blood:

Variant related genes	Relation type
ENSG00000258017	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000139636	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1039225	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.84[TSI][hapmap]
rs10747561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747562	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747563	0.94[CHB][hapmap]
rs10783302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783304	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783306	0.82[ASN][1000 genomes]
rs10783307	0.83[CEU][hapmap];0.81[ASN][1000 genomes]
rs10783308	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs10875924	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10875928	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap]
rs10875931	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs10875934	0.94[CHB][hapmap]
rs11168854	0.81[EUR][1000 genomes]
rs11168857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168862	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168874	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168884	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs11168888	0.81[EUR][1000 genomes]
rs11168893	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs11168895	0.81[EUR][1000 genomes]
rs11168910	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs11837207	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12228775	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229524	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs1476137	0.88[CEU][hapmap];0.91[ASN][1000 genomes]
rs1476138	0.84[ASN][1000 genomes]
rs1874908	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs1991427	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2047101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2162644	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2241727	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2334930	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs2753	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35884657	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57853986	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7306084	0.94[CHB][hapmap]
rs73110168	0.83[ASN][1000 genomes]
rs731350	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7954521	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap]
rs7954530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap]
rs7957983	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957998	0.87[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7958241	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7958572	0.92[CEU][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959497	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap]
rs7969963	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969967	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976890	0.91[ASN][1000 genomes]
rs7978448	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7978659	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9325145	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs9788139	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9788140	0.82[EUR][1000 genomes];0.89[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3741621	POU6F1	cis	parietal	SCAN
rs3741621	TFCP2	cis	parietal	SCAN
rs3741621	C19orf55	trans	cerebellum	SCAN
rs3741621	RHEBL1	cis	parietal	SCAN
rs3741621	CCDC65	cis	Artery Aorta	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49482800-49499200	Weak transcription	Hela-S3	cervix
2	chr12:49489000-49494800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:49489200-49498200	Weak transcription	Right Atrium	heart
4	chr12:49489400-49496600	Strong transcription	Right Ventricle	heart
5	chr12:49489400-49499800	Strong transcription	Fetal Intestine Large	intestine
6	chr12:49489400-49501200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:49489400-49501400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:49489600-49497400	Strong transcription	Adipose Nuclei	Adipose
9	chr12:49489600-49497800	Strong transcription	Fetal Muscle Leg	muscle
10	chr12:49489600-49498400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:49489600-49498400	Strong transcription	Left Ventricle	heart
12	chr12:49489600-49498600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:49489600-49499400	Strong transcription	Fetal Intestine Small	intestine
14	chr12:49489600-49499600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:49489600-49500800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:49489600-49500800	Strong transcription	Thymus	Thymus
17	chr12:49489600-49501200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:49489600-49502800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:49489800-49497400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:49489800-49498600	Strong transcription	Brain Germinal Matrix	brain
21	chr12:49489800-49498800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:49489800-49499400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:49489800-49500000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:49489800-49500600	Strong transcription	Liver	Liver
25	chr12:49489800-49501000	Weak transcription	Fetal Heart	heart
26	chr12:49489800-49502000	Strong transcription	Fetal Stomach	stomach
27	chr12:49490000-49503000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:49490200-49496400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:49490200-49497400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:49490200-49498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr12:49490200-49499000	Strong transcription	Fetal Brain Female	brain
32	chr12:49490200-49501200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:49490400-49495200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:49490400-49498400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:49490400-49498400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:49490400-49498600	Strong transcription	Colon Smooth Muscle	Colon
37	chr12:49490400-49498800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr12:49490400-49498800	Strong transcription	Brain Hippocampus Middle	brain
39	chr12:49490400-49499000	Strong transcription	Fetal Thymus	thymus
40	chr12:49490400-49499400	Strong transcription	Brain Anterior Caudate	brain
41	chr12:49490400-49499400	Strong transcription	Ovary	ovary
42	chr12:49490400-49500200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr12:49490400-49500800	Strong transcription	Primary T cells from cord blood	blood
44	chr12:49490400-49500800	Strong transcription	Colonic Mucosa	Colon
45	chr12:49490400-49500800	Strong transcription	HSMMtube	muscle
46	chr12:49490400-49501000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:49490400-49501200	Strong transcription	Primary B cells from cord blood	blood
48	chr12:49490400-49501200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:49490400-49501400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:49490400-49501600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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