Variant report

Variant	rs785485
Chromosome Location	chr1:46574424-46574425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:46567386..46569330-chr1:46574210..46576052,2	MCF-7	breast:
2	chr1:46573286..46575811-chr1:46596829..46599703,2	MCF-7	breast:
3	chr1:46572890..46576419-chr1:46595522..46598974,5	K562	blood:
4	chr1:46572493..46576559-chr1:46596438..46599521,4	K562	blood:
5	chr1:46573789..46575694-chr1:46576849..46579636,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117461	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10789481	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs10789487	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs1085242	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1085243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1085244	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10890383	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11211230	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs11211251	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11211252	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579634	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs11589562	0.96[CEU][hapmap];0.85[JPT][hapmap];0.80[YRI][hapmap]
rs11810993	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs12021587	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap]
rs12049588	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs12132540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12561806	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap]
rs12564541	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs1355642	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1612092	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1707304	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1707308	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1707321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1707333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1707334	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1707335	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1707336	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs1707340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1768803	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1768809	0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1768816	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2275426	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs2486445	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2486447	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4073846	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs4076006	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs4660342	0.83[ASN][1000 genomes]
rs4660910	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4660911	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6662641	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669522	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs6675726	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6677007	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap]
rs6686134	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap]
rs7522601	1.00[CEU][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap]
rs785464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785471	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs785472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs785473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs785479	0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs785481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs785482	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785488	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785492	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785498	0.97[ASN][1000 genomes]
rs785502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs785503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs785508	0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs785509	0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs785511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785512	0.82[CHB][hapmap]
rs785513	0.88[ASN][1000 genomes]
rs785515	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs785520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809774	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs809775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429088	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9429094	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9429183	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9429189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946529	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
12	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
14	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
15	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs785485	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs785485	CCDC163P	cis	lung	GTEx
rs785485	CCDC163P	cis	Esophagus Muscularis	GTEx
rs785485	CCDC163P	cis	Stomach	GTEx
rs785485	CCDC163P	cis	Esophagus Mucosa	GTEx
rs785485	MAST2	cis	Artery Tibial	GTEx
rs785485	CCDC163P	cis	Artery Tibial	GTEx
rs785485	MAST2	cis	Artery Aorta	GTEx
rs785485	CCDC163P	cis	Muscle Skeletal	GTEx
rs785485	GPBP1L1	cis	Lymphoblastoid	GTEx
rs785485	Hs.396207	cis	multi-tissue	Pritchard
rs785485	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs785485	CCDC163P	cis	Thyroid	GTEx
rs785485	CCDC163P	cis	Heart Left Ventricle	GTEx
rs785485	CCDC163P	cis	Whole Blood	GTEx
rs785485	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs785485	CCDC163P	cis	Artery Aorta	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46532400-46575200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:46540400-46595200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:46541200-46595800	Weak transcription	Fetal Intestine Small	intestine
4	chr1:46553600-46577000	Weak transcription	Left Ventricle	heart
5	chr1:46562000-46578600	Weak transcription	Fetal Brain Female	brain
6	chr1:46562400-46595800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:46565400-46576600	Weak transcription	Dnd41	blood
8	chr1:46565600-46593200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:46566800-46580600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:46566800-46594000	Weak transcription	Thymus	Thymus
11	chr1:46567400-46576200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:46567800-46580600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr1:46567800-46595200	Weak transcription	Primary T cells from cord blood	blood
14	chr1:46568800-46575800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:46569000-46581400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:46569200-46575600	Weak transcription	Hela-S3	cervix
17	chr1:46569200-46578200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:46572400-46576400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:46572600-46575400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:46572600-46580600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:46572800-46579800	Weak transcription	Right Atrium	heart
22	chr1:46573600-46574800	Enhancers	GM12878-XiMat	blood
23	chr1:46574000-46595200	Weak transcription	HSMM	muscle

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