Variant report

Variant	rs56223447
Chromosome Location	chr1:224561479-224561480
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224561356..224563352-chr1:224578652..224580931,2	K562	blood:
2	chr1:224551974..224553710-chr1:224558938..224561621,2	K562	blood:
3	chr1:224559948..224562701-chr1:224564566..224567149,2	K562	blood:
4	chr1:224544372..224546444-chr1:224561332..224563274,2	K562	blood:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10127813	0.99[EUR][1000 genomes]
rs10127953	0.99[EUR][1000 genomes]
rs10128058	0.99[EUR][1000 genomes]
rs10159333	0.88[EUR][1000 genomes]
rs10495219	0.90[EUR][1000 genomes]
rs10753465	0.99[EUR][1000 genomes]
rs10753466	0.99[EUR][1000 genomes]
rs10753467	0.86[EUR][1000 genomes]
rs10753468	0.86[EUR][1000 genomes]
rs10799569	0.99[EUR][1000 genomes]
rs10916606	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916607	0.99[EUR][1000 genomes]
rs10916614	0.89[EUR][1000 genomes]
rs10916616	0.88[EUR][1000 genomes]
rs10916617	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916619	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11576835	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11577170	0.86[EUR][1000 genomes]
rs11577183	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11579952	0.96[EUR][1000 genomes]
rs11584247	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11584638	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11584980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11586729	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11588973	0.85[EUR][1000 genomes]
rs11590658	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11800613	0.86[EUR][1000 genomes]
rs11801436	0.96[EUR][1000 genomes]
rs11801645	0.96[EUR][1000 genomes]
rs11803414	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11803981	0.96[EUR][1000 genomes]
rs11805973	0.84[EUR][1000 genomes]
rs11807763	0.87[EUR][1000 genomes]
rs11807942	0.99[EUR][1000 genomes]
rs11811053	0.95[EUR][1000 genomes]
rs12062871	0.84[EUR][1000 genomes]
rs12731035	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12731630	0.86[EUR][1000 genomes]
rs12738799	0.90[EUR][1000 genomes]
rs12739486	0.90[EUR][1000 genomes]
rs12740255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12742821	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12742989	0.88[EUR][1000 genomes]
rs12743200	0.86[EUR][1000 genomes]
rs12745610	0.99[EUR][1000 genomes]
rs12747286	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12751161	0.90[EUR][1000 genomes]
rs12754832	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12755338	0.82[EUR][1000 genomes]
rs12755816	0.99[EUR][1000 genomes]
rs12758302	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12758579	0.86[EUR][1000 genomes]
rs12759275	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1539207	0.99[EUR][1000 genomes]
rs1544196	0.84[EUR][1000 genomes]
rs16848365	0.86[EUR][1000 genomes]
rs17503938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2185684	0.86[EUR][1000 genomes]
rs28434172	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2897048	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35011635	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35031726	0.99[EUR][1000 genomes]
rs35067427	0.86[EUR][1000 genomes]
rs35169600	0.97[EUR][1000 genomes]
rs35277713	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35303987	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35341841	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35365551	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35571080	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35915186	0.81[EUR][1000 genomes]
rs35972228	0.96[EUR][1000 genomes]
rs36138926	0.99[EUR][1000 genomes]
rs4653587	0.88[EUR][1000 genomes]
rs4654037	0.99[EUR][1000 genomes]
rs55730749	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6426121	0.96[EUR][1000 genomes]
rs6426123	0.88[EUR][1000 genomes]
rs6426125	0.88[EUR][1000 genomes]
rs6426126	0.88[EUR][1000 genomes]
rs66467176	0.85[EUR][1000 genomes]
rs6663522	0.86[EUR][1000 genomes]
rs6671751	0.96[EUR][1000 genomes]
rs6672859	0.99[EUR][1000 genomes]
rs6675858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691779	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6693287	0.98[EUR][1000 genomes]
rs6701145	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67065875	0.96[EUR][1000 genomes]
rs68037178	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71644786	0.84[AMR][1000 genomes]
rs7365151	0.85[EUR][1000 genomes]
rs7512431	0.99[EUR][1000 genomes]
rs7513208	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7514284	0.96[EUR][1000 genomes]
rs7514575	0.86[EUR][1000 genomes]
rs7517754	0.96[EUR][1000 genomes]
rs7518109	0.99[EUR][1000 genomes]
rs7519734	0.96[EUR][1000 genomes]
rs7522956	0.99[EUR][1000 genomes]
rs7527044	0.90[EUR][1000 genomes]
rs7529067	0.96[EUR][1000 genomes]
rs7529310	0.88[EUR][1000 genomes]
rs867362	0.86[EUR][1000 genomes]
rs885606	0.86[EUR][1000 genomes]
rs9970697	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs56223447	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs56223447	CNIH4	cis	Esophagus Muscularis	GTEx
rs56223447	CNIH4	cis	Heart Left Ventricle	GTEx
rs56223447	CNIH4	cis	Muscle Skeletal	GTEx
rs56223447	CNIH4	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
3	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:224546800-224562200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
7	chr1:224547400-224561800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:224547800-224562800	Weak transcription	Pancreas	Pancrea
10	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
12	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:224550800-224564200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:224550800-224565000	Strong transcription	HUVEC	blood vessel
15	chr1:224551000-224568000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:224551200-224563600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:224551200-224565800	Strong transcription	Primary B cells from cord blood	blood
18	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:224551600-224566600	Strong transcription	Dnd41	blood
20	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:224551800-224561600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:224552000-224564800	Weak transcription	Psoas Muscle	Psoas
24	chr1:224552600-224563800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:224552800-224562000	Strong transcription	Osteobl	bone
26	chr1:224552800-224564200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:224552800-224565800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:224553000-224562800	Strong transcription	Fetal Thymus	thymus
29	chr1:224553000-224562800	Strong transcription	HSMM	muscle
30	chr1:224553000-224564200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:224553000-224565000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:224553000-224565200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:224553200-224562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:224553200-224562800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:224553200-224564400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:224553400-224562200	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:224553400-224562400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:224553400-224565000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:224553400-224567000	Strong transcription	Adipose Nuclei	Adipose
41	chr1:224553400-224567400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr1:224553600-224564400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:224553600-224566000	Strong transcription	Fetal Intestine Large	intestine
44	chr1:224553600-224566400	Strong transcription	Fetal Intestine Small	intestine
45	chr1:224553800-224564200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
47	chr1:224554200-224565600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr1:224554400-224563600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:224554400-224568200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:224554600-224564200	Strong transcription	NHDF-Ad	bronchial

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