Variant report

Variant	rs72704652
Chromosome Location	chr1:150819470-150819471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150598853..150601139-chr1:150818426..150820155,2	K562	blood:
2	chr1:150818986..150820930-chr1:150847610..150849442,2	MCF-7	breast:
3	chr1:150818101..150820451-chr1:150845957..150847581,2	K562	blood:
4	chr1:150818877..150820546-chr1:151019775..151022165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143443	Chromatin interaction
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1027699	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305664	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10305667	0.82[ASN][1000 genomes]
rs10305672	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305673	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305704	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305714	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10305720	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10399947	0.92[EUR][1000 genomes]
rs10788794	0.81[EUR][1000 genomes]
rs10888391	0.81[EUR][1000 genomes]
rs10888392	0.84[EUR][1000 genomes]
rs10888393	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10888394	0.84[EUR][1000 genomes]
rs10888395	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10888397	0.91[EUR][1000 genomes]
rs10888398	0.84[EUR][1000 genomes]
rs11204722	0.81[EUR][1000 genomes]
rs11204723	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204726	0.84[EUR][1000 genomes]
rs11204733	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204739	0.93[EUR][1000 genomes]
rs11204742	0.90[EUR][1000 genomes]
rs11204743	0.81[EUR][1000 genomes]
rs11204750	0.84[EUR][1000 genomes]
rs11552229	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11581757	0.91[EUR][1000 genomes]
rs11582281	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11589458	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589886	0.80[EUR][1000 genomes]
rs11800855	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12059949	0.84[EUR][1000 genomes]
rs12068264	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12075597	0.80[EUR][1000 genomes]
rs12085336	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12090215	0.91[EUR][1000 genomes]
rs12096831	0.94[EUR][1000 genomes]
rs12097963	0.93[EUR][1000 genomes]
rs12404949	0.81[EUR][1000 genomes]
rs12406660	0.81[ASN][1000 genomes]
rs12409208	0.94[EUR][1000 genomes]
rs12410394	0.94[EUR][1000 genomes]
rs12410869	0.86[EUR][1000 genomes]
rs1532770	0.80[EUR][1000 genomes]
rs1546376	0.84[EUR][1000 genomes]
rs16827671	0.84[EUR][1000 genomes]
rs17660092	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889740	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1889741	0.85[EUR][1000 genomes]
rs2089082	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124952	0.85[EUR][1000 genomes]
rs2228099	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2230061	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2256355	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272214	0.85[EUR][1000 genomes]
rs2275235	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2864869	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2864871	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2864873	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2864882	0.84[EUR][1000 genomes]
rs2867296	0.85[EUR][1000 genomes]
rs34985895	0.84[EUR][1000 genomes]
rs36008098	0.86[EUR][1000 genomes]
rs3754212	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3768013	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768015	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768016	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3768018	0.81[EUR][1000 genomes]
rs3843843	0.85[EUR][1000 genomes]
rs4319334	0.81[ASN][1000 genomes]
rs4451553	0.81[EUR][1000 genomes]
rs4509581	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4537557	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4970928	0.87[EUR][1000 genomes]
rs4970929	0.86[EUR][1000 genomes]
rs4970930	0.91[EUR][1000 genomes]
rs4970980	0.86[EUR][1000 genomes]
rs4970982	0.94[EUR][1000 genomes]
rs4970984	0.84[EUR][1000 genomes]
rs4970985	0.84[EUR][1000 genomes]
rs4970986	0.86[EUR][1000 genomes]
rs57818453	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59024312	0.86[EUR][1000 genomes]
rs59337856	0.84[EUR][1000 genomes]
rs6657388	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6658066	0.82[EUR][1000 genomes]
rs6660084	0.84[EUR][1000 genomes]
rs6660845	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669855	0.92[EUR][1000 genomes]
rs6671737	0.91[EUR][1000 genomes]
rs66847267	0.84[EUR][1000 genomes]
rs6693120	0.87[EUR][1000 genomes]
rs72704639	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72704654	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704656	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704658	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72704679	0.82[EUR][1000 genomes]
rs72704682	0.88[EUR][1000 genomes]
rs72704685	0.87[EUR][1000 genomes]
rs7514004	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521592	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526489	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7528773	0.86[EUR][1000 genomes]
rs7532045	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556661	0.91[EUR][1000 genomes]
rs8444	0.84[EUR][1000 genomes]
rs897815	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv872420	chr1:150786038-150847647	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1010875	chr1:150796816-150845827	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv1793983	chr1:150804748-150825924	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs72704652	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs72704652	CTSS	cis	Artery Tibial	GTEx
rs72704652	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs72704652	RP11-316M1.12	cis	Artery Aorta	GTEx
rs72704652	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs72704652	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs72704652	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs72704652	RP11-316M1.12	cis	lung	GTEx
rs72704652	HORMAD1	cis	Nerve Tibial	GTEx
rs72704652	GOLPH3L	cis	Nerve Tibial	GTEx
rs72704652	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs72704652	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs72704652	RP11-316M1.12	cis	Thyroid	GTEx
rs72704652	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs72704652	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs72704652	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs72704652	RP11-316M1.12	cis	Whole Blood	GTEx
rs72704652	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs72704652	CTSS	cis	Thyroid	GTEx
rs72704652	RP11-316M1.12	cis	Artery Tibial	GTEx
rs72704652	HORMAD1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150793200-150823200	Strong transcription	Placenta	Placenta
2	chr1:150801800-150824600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:150805800-150824600	Weak transcription	HMEC	breast
4	chr1:150807200-150820800	Weak transcription	Spleen	Spleen
5	chr1:150807400-150824600	Weak transcription	A549	lung
6	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
7	chr1:150808000-150821600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
9	chr1:150809000-150823000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:150809000-150824400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:150809000-150824600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:150809200-150820600	Weak transcription	Brain Germinal Matrix	brain
13	chr1:150809200-150824600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:150809400-150821000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:150809400-150821000	Weak transcription	Thymus	Thymus
17	chr1:150809400-150823200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:150809600-150820400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
20	chr1:150810000-150824800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:150810200-150824600	Weak transcription	NHLF	lung
22	chr1:150810400-150846600	Weak transcription	Fetal Heart	heart
23	chr1:150812000-150824400	Weak transcription	Fetal Brain Male	brain
24	chr1:150812000-150831200	Weak transcription	Lung	lung
25	chr1:150812000-150847000	Weak transcription	Gastric	stomach
26	chr1:150812200-150821600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:150812200-150822200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:150812200-150824600	Weak transcription	HepG2	liver
29	chr1:150812200-150824600	Weak transcription	NHEK	skin
30	chr1:150812200-150828000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:150812200-150829800	Weak transcription	HUVEC	blood vessel
32	chr1:150812200-150834000	Weak transcription	Brain Angular Gyrus	brain
33	chr1:150812400-150820000	Weak transcription	Brain Anterior Caudate	brain
34	chr1:150812400-150820000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:150812400-150820600	Weak transcription	Aorta	Aorta
36	chr1:150812400-150820600	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:150812400-150821600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:150812400-150824400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:150812400-150824400	Weak transcription	Dnd41	blood
40	chr1:150812400-150824400	Weak transcription	GM12878-XiMat	blood
41	chr1:150812400-150824600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:150812400-150824600	Weak transcription	Brain Substantia Nigra	brain
43	chr1:150812400-150824600	Weak transcription	NH-A	brain
44	chr1:150812400-150830800	Weak transcription	Ovary	ovary
45	chr1:150812400-150840600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:150812400-150842000	Weak transcription	Esophagus	oesophagus
47	chr1:150812400-150846800	Weak transcription	Fetal Kidney	kidney
48	chr1:150812600-150820600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:150812600-150820600	Weak transcription	Fetal Stomach	stomach
50	chr1:150812600-150821000	Weak transcription	Stomach Smooth Muscle	stomach

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