Variant report

Variant	rs72704656
Chromosome Location	chr1:150828307-150828308
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	chr1:150825805..150828519-chr1:150980841..150983000,2	K562	blood:

Variant related genes	Relation type
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1027699	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10305664	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10305667	0.83[ASN][1000 genomes]
rs10305672	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10305673	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10305704	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10305711	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10305714	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10305720	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10399947	0.89[EUR][1000 genomes]
rs10788794	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10888391	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10888392	0.89[EUR][1000 genomes]
rs10888393	0.83[EUR][1000 genomes]
rs10888394	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10888395	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10888397	0.85[EUR][1000 genomes]
rs10888398	0.91[EUR][1000 genomes]
rs11204722	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11204723	0.82[EUR][1000 genomes]
rs11204726	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204733	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204739	0.86[EUR][1000 genomes]
rs11204742	0.84[EUR][1000 genomes]
rs11204747	0.85[EUR][1000 genomes]
rs11204748	0.84[EUR][1000 genomes]
rs11204749	0.85[EUR][1000 genomes]
rs11552229	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11581757	0.85[EUR][1000 genomes]
rs11582281	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11589458	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11589886	0.87[EUR][1000 genomes]
rs11800855	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12068264	0.81[EUR][1000 genomes]
rs12075597	0.87[EUR][1000 genomes]
rs12085336	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12090215	0.85[EUR][1000 genomes]
rs12096831	0.87[EUR][1000 genomes]
rs12097963	0.86[EUR][1000 genomes]
rs12406660	0.83[ASN][1000 genomes]
rs12409208	0.87[EUR][1000 genomes]
rs12410394	0.87[EUR][1000 genomes]
rs12410869	0.94[EUR][1000 genomes]
rs1532770	0.87[EUR][1000 genomes]
rs16827671	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17660092	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1889740	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1889741	0.93[EUR][1000 genomes]
rs1972060	0.84[EUR][1000 genomes]
rs2089082	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2228099	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2230061	0.81[EUR][1000 genomes]
rs2256355	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271076	0.86[EUR][1000 genomes]
rs2275235	0.82[EUR][1000 genomes]
rs2280627	0.84[EUR][1000 genomes]
rs2864869	0.82[EUR][1000 genomes]
rs2864871	0.83[AFR][1000 genomes]
rs2864873	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864882	0.91[EUR][1000 genomes]
rs2867297	0.86[EUR][1000 genomes]
rs36008098	0.93[EUR][1000 genomes]
rs3754212	0.83[EUR][1000 genomes]
rs3768013	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768015	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3768016	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3768018	0.88[EUR][1000 genomes]
rs3849279	0.82[EUR][1000 genomes]
rs4319334	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4509581	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4537557	0.82[EUR][1000 genomes]
rs4970928	0.81[EUR][1000 genomes]
rs4970930	0.84[EUR][1000 genomes]
rs4970931	0.86[EUR][1000 genomes]
rs4970980	0.94[EUR][1000 genomes]
rs4970982	0.87[EUR][1000 genomes]
rs4970984	0.91[EUR][1000 genomes]
rs4970985	0.91[EUR][1000 genomes]
rs57818453	0.85[EUR][1000 genomes]
rs59337856	0.90[EUR][1000 genomes]
rs6587542	0.86[EUR][1000 genomes]
rs6657388	0.83[EUR][1000 genomes]
rs6660084	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6660845	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6669855	0.89[EUR][1000 genomes]
rs6671737	0.83[EUR][1000 genomes]
rs66847267	0.91[EUR][1000 genomes]
rs6686064	0.86[EUR][1000 genomes]
rs72704639	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72704652	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72704654	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704658	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72704679	0.89[EUR][1000 genomes]
rs72704682	0.82[EUR][1000 genomes]
rs72704685	0.81[EUR][1000 genomes]
rs7514004	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518156	0.81[EUR][1000 genomes]
rs7521592	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752376	0.82[EUR][1000 genomes]
rs7526489	0.81[EUR][1000 genomes]
rs7532045	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7556451	0.85[EUR][1000 genomes]
rs7556661	0.85[EUR][1000 genomes]
rs897815	0.84[EUR][1000 genomes]
rs9661876	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs72704656	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs72704656	CTSS	cis	Artery Tibial	GTEx
rs72704656	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs72704656	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs72704656	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs72704656	HORMAD1	cis	Nerve Tibial	GTEx
rs72704656	RP11-316M1.12	cis	Thyroid	GTEx
rs72704656	RP11-316M1.12	cis	Artery Tibial	GTEx
rs72704656	CTSS	cis	Thyroid	GTEx
rs72704656	HORMAD1	cis	Esophagus Mucosa	GTEx
rs72704656	RP11-316M1.12	cis	Whole Blood	GTEx
rs72704656	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs72704656	GOLPH3L	cis	Nerve Tibial	GTEx
rs72704656	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs72704656	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs72704656	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs72704656	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs72704656	RP11-316M1.12	cis	lung	GTEx
rs72704656	RP11-316M1.12	cis	Artery Aorta	GTEx
rs72704656	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs72704656	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150807400-150847000	Weak transcription	Colonic Mucosa	Colon
2	chr1:150808800-150847000	Weak transcription	Psoas Muscle	Psoas
3	chr1:150809200-150846800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:150809600-150846000	Weak transcription	Pancreas	Pancrea
5	chr1:150810400-150846600	Weak transcription	Fetal Heart	heart
6	chr1:150812000-150831200	Weak transcription	Lung	lung
7	chr1:150812000-150847000	Weak transcription	Gastric	stomach
8	chr1:150812200-150829800	Weak transcription	HUVEC	blood vessel
9	chr1:150812200-150834000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:150812400-150830800	Weak transcription	Ovary	ovary
11	chr1:150812400-150840600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:150812400-150842000	Weak transcription	Esophagus	oesophagus
13	chr1:150812400-150846800	Weak transcription	Fetal Kidney	kidney
14	chr1:150812600-150846000	Weak transcription	Small Intestine	intestine
15	chr1:150812600-150846800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:150814600-150833400	Weak transcription	Hela-S3	cervix
17	chr1:150814800-150839600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:150815200-150832000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:150815400-150842400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:150815400-150846800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:150815600-150838000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:150816600-150829200	Weak transcription	HSMM	muscle
23	chr1:150819600-150831200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:150820600-150846800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:150821200-150846600	Weak transcription	Aorta	Aorta
26	chr1:150821200-150846600	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:150821200-150846800	Weak transcription	Brain Anterior Caudate	brain
28	chr1:150821200-150848600	Weak transcription	Spleen	Spleen
29	chr1:150822400-150829600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:150822400-150846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:150824000-150830600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:150824200-150829400	Strong transcription	Fetal Stomach	stomach
33	chr1:150824200-150831000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:150824400-150828400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:150824400-150828400	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:150824400-150828600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr1:150824400-150829400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:150824400-150829600	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:150824400-150830800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:150824400-150830800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:150824400-150831000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:150824400-150831000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:150824400-150831200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:150824400-150831200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr1:150824600-150828400	Strong transcription	Brain Germinal Matrix	brain
46	chr1:150824600-150828400	Strong transcription	Fetal Intestine Large	intestine
47	chr1:150824600-150829400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:150824600-150830000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:150824600-150830800	Strong transcription	Primary T cells from cord blood	blood
50	chr1:150824600-150830800	Strong transcription	Primary T helper cells PMA-I stimulated	--

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