Variant report

Variant	rs6672859
Chromosome Location	chr1:224572470-224572471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224565954..224567779-chr1:224572206..224574847,2	K562	blood:
2	chr1:224570866..224573181-chr1:224620573..224622474,2	K562	blood:
3	chr1:224570342..224572571-chr1:224573796..224575768,2	K562	blood:
4	chr1:224572039..224576189-chr1:224576688..224579602,3	K562	blood:

Variant related genes	Relation type
ENSG00000162923	Chromatin interaction
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10127813	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10127953	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10128058	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159333	0.89[EUR][1000 genomes]
rs10495219	0.90[EUR][1000 genomes]
rs10753465	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753466	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10753467	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10753468	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10799569	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10916606	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916607	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916614	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916616	0.89[EUR][1000 genomes]
rs10916617	0.86[EUR][1000 genomes]
rs10916619	0.86[EUR][1000 genomes]
rs11576835	0.99[EUR][1000 genomes]
rs11577170	0.86[EUR][1000 genomes]
rs11577183	0.99[EUR][1000 genomes]
rs11579952	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11584247	0.96[EUR][1000 genomes]
rs11584638	0.88[EUR][1000 genomes]
rs11584980	0.99[EUR][1000 genomes]
rs11586729	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588973	0.86[EUR][1000 genomes]
rs11590658	0.86[EUR][1000 genomes]
rs11800613	0.86[EUR][1000 genomes]
rs11801436	0.97[EUR][1000 genomes]
rs11801645	0.97[EUR][1000 genomes]
rs11803414	0.98[EUR][1000 genomes]
rs11803981	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11805973	0.85[EUR][1000 genomes]
rs11807763	0.88[EUR][1000 genomes]
rs11807942	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11811053	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062871	0.85[EUR][1000 genomes]
rs12731035	0.96[EUR][1000 genomes]
rs12731630	0.86[EUR][1000 genomes]
rs12738799	0.90[EUR][1000 genomes]
rs12739486	0.90[EUR][1000 genomes]
rs12740255	0.99[EUR][1000 genomes]
rs12742821	0.99[EUR][1000 genomes]
rs12742989	0.88[EUR][1000 genomes]
rs12743200	0.86[EUR][1000 genomes]
rs12745610	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747286	0.90[EUR][1000 genomes]
rs12751161	0.90[EUR][1000 genomes]
rs12754832	0.99[EUR][1000 genomes]
rs12755338	0.83[EUR][1000 genomes]
rs12755816	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12758302	0.83[EUR][1000 genomes]
rs12758579	0.86[EUR][1000 genomes]
rs12759275	0.99[EUR][1000 genomes]
rs1539207	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544196	0.85[EUR][1000 genomes]
rs16848365	0.86[EUR][1000 genomes]
rs17503938	0.99[EUR][1000 genomes]
rs2185684	0.86[EUR][1000 genomes]
rs28434172	0.88[EUR][1000 genomes]
rs2897048	0.89[EUR][1000 genomes]
rs35011635	0.88[EUR][1000 genomes]
rs35031726	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35067427	0.86[EUR][1000 genomes]
rs35169600	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35277713	0.88[EUR][1000 genomes]
rs35303987	0.88[EUR][1000 genomes]
rs35341841	0.96[EUR][1000 genomes]
rs35365551	0.84[EUR][1000 genomes]
rs35571080	0.86[EUR][1000 genomes]
rs35915186	0.82[EUR][1000 genomes]
rs35972228	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36138926	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653585	0.89[AFR][1000 genomes]
rs4653587	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4654037	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55730749	0.86[EUR][1000 genomes]
rs56223447	0.99[EUR][1000 genomes]
rs6426121	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426123	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426125	0.89[EUR][1000 genomes]
rs6426126	0.89[EUR][1000 genomes]
rs66467176	0.86[EUR][1000 genomes]
rs6663522	0.86[EUR][1000 genomes]
rs6671751	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6675858	0.99[EUR][1000 genomes]
rs6691779	0.99[EUR][1000 genomes]
rs6693287	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701145	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67065875	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68037178	0.98[EUR][1000 genomes]
rs7365151	0.86[EUR][1000 genomes]
rs7512431	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7513208	0.96[EUR][1000 genomes]
rs7514284	0.97[EUR][1000 genomes]
rs7514575	0.87[EUR][1000 genomes]
rs7517754	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7518109	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7519734	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7522956	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527044	0.91[EUR][1000 genomes]
rs7529067	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7529310	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs867362	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs885606	0.86[EUR][1000 genomes]
rs9970697	0.83[AMR][1000 genomes];0.85[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6672859	CNIH4	cis	Heart Left Ventricle	GTEx
rs6672859	CNIH4	cis	Nerve Tibial	GTEx
rs6672859	CNIH4	cis	Esophagus Muscularis	GTEx
rs6672859	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs6672859	CNIH4	cis	Adipose Subcutaneous	GTEx
rs6672859	CNIH4	cis	Thyroid	GTEx
rs6672859	CNIH4	cis	Esophagus Mucosa	GTEx
rs6672859	CNIH4	cis	Stomach	GTEx
rs6672859	CNIH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
3	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
5	chr1:224555800-224581400	Weak transcription	Fetal Heart	heart
6	chr1:224556000-224591000	Weak transcription	Small Intestine	intestine
7	chr1:224563000-224577200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:224563000-224593400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:224564600-224576600	Weak transcription	Ovary	ovary
10	chr1:224565000-224575000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr1:224565000-224575800	Weak transcription	Brain Angular Gyrus	brain
12	chr1:224565000-224576800	Weak transcription	NHEK	skin
13	chr1:224565000-224577200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:224565000-224577200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:224565000-224577200	Weak transcription	Colonic Mucosa	Colon
16	chr1:224565000-224577200	Weak transcription	Pancreas	Pancrea
17	chr1:224565000-224577200	Weak transcription	Spleen	Spleen
18	chr1:224565000-224581200	Weak transcription	Right Ventricle	heart
19	chr1:224565000-224582600	Weak transcription	Esophagus	oesophagus
20	chr1:224565000-224586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:224565200-224574600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:224565200-224576000	Weak transcription	Hela-S3	cervix
23	chr1:224565400-224577000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:224565600-224575000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:224565800-224576600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:224566000-224574600	Weak transcription	NHLF	lung
27	chr1:224566000-224576000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:224566000-224576800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:224566200-224573200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:224566200-224575000	Weak transcription	Left Ventricle	heart
31	chr1:224566200-224576400	Weak transcription	HepG2	liver
32	chr1:224566200-224577000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:224566200-224577200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:224566400-224577800	Weak transcription	Fetal Intestine Small	intestine
35	chr1:224567000-224577400	Weak transcription	Lung	lung
36	chr1:224567000-224577600	Weak transcription	Gastric	stomach
37	chr1:224567000-224579600	Weak transcription	Psoas Muscle	Psoas
38	chr1:224567200-224573800	Weak transcription	Liver	Liver
39	chr1:224567200-224574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:224567200-224574000	Weak transcription	Adipose Nuclei	Adipose
41	chr1:224567200-224574800	Weak transcription	A549	lung
42	chr1:224567200-224577000	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:224567400-224572600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:224567400-224573200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:224567400-224575200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr1:224567400-224575200	Weak transcription	Fetal Lung	lung
47	chr1:224567400-224575400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:224567400-224575400	Weak transcription	Brain Substantia Nigra	brain
49	chr1:224567400-224575400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:224567400-224576000	Weak transcription	Fetal Kidney	kidney

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