Variant report

Variant	rs4653587
Chromosome Location	chr1:224628508-224628509
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224543651..224545757-chr1:224626947..224629094,2	MCF-7	breast:
2	chr1:224620725..224622955-chr1:224626744..224628557,4	MCF-7	breast:
3	chr1:224627143..224628933-chr1:224633589..224638837,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162923	Chromatin interaction
ENSG00000143786	Chromatin interaction
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10127813	0.89[EUR][1000 genomes]
rs10127953	0.89[EUR][1000 genomes]
rs10128058	0.89[EUR][1000 genomes]
rs10159333	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495219	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753465	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10753466	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753467	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753468	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10799569	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916606	0.88[EUR][1000 genomes]
rs10916607	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916614	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916616	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916617	0.96[EUR][1000 genomes]
rs10916619	0.96[EUR][1000 genomes]
rs11576835	0.88[EUR][1000 genomes]
rs11577170	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11577183	0.88[EUR][1000 genomes]
rs11578709	0.88[EUR][1000 genomes]
rs11579952	0.89[EUR][1000 genomes]
rs11584057	0.85[EUR][1000 genomes]
rs11584247	0.88[EUR][1000 genomes]
rs11584638	0.99[EUR][1000 genomes]
rs11584980	0.88[EUR][1000 genomes]
rs11586729	0.88[EUR][1000 genomes]
rs11588973	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11590658	0.96[EUR][1000 genomes]
rs11800613	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11801436	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801645	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803414	0.90[EUR][1000 genomes]
rs11803981	0.89[EUR][1000 genomes]
rs11805973	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807763	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807942	0.88[EUR][1000 genomes]
rs11811053	0.85[EUR][1000 genomes]
rs12062871	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12731035	0.91[EUR][1000 genomes]
rs12731630	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12738799	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739486	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740255	0.88[EUR][1000 genomes]
rs12742821	0.88[EUR][1000 genomes]
rs12742989	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12743200	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12745610	0.89[EUR][1000 genomes]
rs12747286	0.96[EUR][1000 genomes]
rs12751161	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754832	0.88[EUR][1000 genomes]
rs12755338	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12755816	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758302	0.94[EUR][1000 genomes]
rs12758579	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12759275	0.88[EUR][1000 genomes]
rs1539207	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1544196	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848365	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503938	0.88[EUR][1000 genomes]
rs17570292	0.86[EUR][1000 genomes]
rs2185684	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28434172	0.96[EUR][1000 genomes]
rs2897048	0.97[EUR][1000 genomes]
rs34791963	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35011635	0.99[EUR][1000 genomes]
rs35031726	0.89[EUR][1000 genomes]
rs35067427	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35169600	0.87[EUR][1000 genomes]
rs35277713	0.99[EUR][1000 genomes]
rs35303987	0.99[EUR][1000 genomes]
rs35341841	0.85[EUR][1000 genomes]
rs35365551	0.95[EUR][1000 genomes]
rs35571080	0.96[EUR][1000 genomes]
rs35767322	0.89[EUR][1000 genomes]
rs35804313	0.88[EUR][1000 genomes]
rs35915186	0.92[EUR][1000 genomes]
rs35972228	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36138926	0.89[EUR][1000 genomes]
rs4654037	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55730749	0.96[EUR][1000 genomes]
rs56223447	0.88[EUR][1000 genomes]
rs6426121	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426123	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426125	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6426126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467176	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6663522	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6671751	0.89[EUR][1000 genomes]
rs6672859	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6675858	0.88[EUR][1000 genomes]
rs6691779	0.88[EUR][1000 genomes]
rs6693287	0.88[EUR][1000 genomes]
rs6698343	0.86[EUR][1000 genomes]
rs6701145	0.88[EUR][1000 genomes]
rs67065875	0.89[EUR][1000 genomes]
rs68037178	0.87[EUR][1000 genomes]
rs71644786	0.90[EUR][1000 genomes]
rs7365151	0.96[EUR][1000 genomes]
rs7512431	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513208	0.88[EUR][1000 genomes]
rs7514284	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514575	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517754	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7518109	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519734	0.89[EUR][1000 genomes]
rs7522956	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527044	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529067	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7529310	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885606	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970697	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4653587	CNIH4	cis	Muscle Skeletal	GTEx
rs4653587	CNIH4	cis	Thyroid	GTEx
rs4653587	CNIH4	cis	Adipose Subcutaneous	GTEx
rs4653587	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs4653587	CNIH4	cis	Nerve Tibial	GTEx
rs4653587	CNIH4	cis	Esophagus Mucosa	GTEx
rs4653587	CNIH4	cis	Stomach	GTEx
rs4653587	CNIH4	cis	Heart Left Ventricle	GTEx
rs4653587	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224623200-224634800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:224623200-224644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224623400-224631600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:224623400-224633400	Weak transcription	Gastric	stomach
5	chr1:224623400-224634600	Weak transcription	Lung	lung
6	chr1:224623400-224634800	Weak transcription	Aorta	Aorta
7	chr1:224623400-224634800	Weak transcription	Left Ventricle	heart
8	chr1:224623400-224634800	Weak transcription	Ovary	ovary
9	chr1:224623400-224634800	Weak transcription	Right Atrium	heart
10	chr1:224623400-224638000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:224623400-224641000	Weak transcription	Fetal Intestine Large	intestine
12	chr1:224623400-224643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:224623400-224644600	Weak transcription	Right Ventricle	heart
14	chr1:224623600-224628800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:224623600-224629800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:224623600-224630400	Weak transcription	Fetal Brain Male	brain
17	chr1:224623600-224635000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:224623600-224635600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:224623600-224636200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:224623600-224637400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:224623600-224642200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr1:224623600-224644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:224623600-224644600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:224623800-224630200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:224623800-224632600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:224623800-224634800	Weak transcription	Stomach Mucosa	stomach
27	chr1:224623800-224635000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr1:224623800-224644400	Weak transcription	Brain Anterior Caudate	brain
29	chr1:224624000-224630400	Weak transcription	Primary B cells from cord blood	blood
30	chr1:224624000-224633000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:224624000-224633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr1:224624000-224634000	Weak transcription	Liver	Liver
33	chr1:224624000-224634600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:224624000-224634600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:224624000-224634800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:224624000-224634800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:224624000-224634800	Weak transcription	HSMMtube	muscle
38	chr1:224624000-224635000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:224624000-224635200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:224624000-224635400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:224624000-224636200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:224624000-224637600	Weak transcription	Fetal Thymus	thymus
43	chr1:224624000-224642200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:224624000-224644000	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:224624000-224644600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:224624000-224644600	Weak transcription	Brain Angular Gyrus	brain
47	chr1:224624000-224645000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:224624000-224645000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:224624000-224645000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr1:224624000-224646800	Weak transcription	Primary B cells from peripheral blood	blood

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