Variant report

Variant	rs12731035
Chromosome Location	chr1:224592880-224592881
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:224592669-224592968	K562	blood:	n/a	n/a
2	POLR2A	chr1:224592297-224593913	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224587420..224589021-chr1:224590396..224593890,3	K562	blood:
2	chr1:224591069..224594043-chr1:224595295..224597255,3	K562	blood:
3	chr1:224592543..224595512-chr1:224595755..224597516,2	K562	blood:
4	chr1:224592158..224594824-chr1:224599014..224600624,2	K562	blood:
5	chr1:224585410..224588248-chr1:224592712..224594281,2	K562	blood:
6	chr1:224592165..224594040-chr1:224621012..224622694,2	MCF-7	breast:

No data

Variant related genes	Relation type
WDR26	TF binding region
ENSG00000266618	Chromatin interaction
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10127813	0.96[EUR][1000 genomes]
rs10127953	0.96[EUR][1000 genomes]
rs10128058	0.96[EUR][1000 genomes]
rs10159333	0.91[EUR][1000 genomes]
rs10495219	0.92[EUR][1000 genomes]
rs10753465	0.96[EUR][1000 genomes]
rs10753466	0.96[EUR][1000 genomes]
rs10753467	0.88[EUR][1000 genomes]
rs10753468	0.88[EUR][1000 genomes]
rs10799569	0.96[EUR][1000 genomes]
rs10916606	0.94[EUR][1000 genomes]
rs10916607	0.96[EUR][1000 genomes]
rs10916614	0.92[EUR][1000 genomes]
rs10916616	0.91[EUR][1000 genomes]
rs10916617	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916619	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11576835	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577170	0.88[EUR][1000 genomes]
rs11577183	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11578709	0.83[AMR][1000 genomes]
rs11579952	0.94[EUR][1000 genomes]
rs11584247	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584638	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584980	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586729	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11588973	0.88[EUR][1000 genomes]
rs11590658	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11800613	0.88[EUR][1000 genomes]
rs11801436	0.99[EUR][1000 genomes]
rs11801645	0.99[EUR][1000 genomes]
rs11803414	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803981	0.94[EUR][1000 genomes]
rs11805973	0.87[EUR][1000 genomes]
rs11807763	0.90[EUR][1000 genomes]
rs11807942	0.96[EUR][1000 genomes]
rs11811053	0.92[EUR][1000 genomes]
rs12062871	0.87[EUR][1000 genomes]
rs12731630	0.88[EUR][1000 genomes]
rs12738799	0.92[EUR][1000 genomes]
rs12739486	0.92[EUR][1000 genomes]
rs12740255	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742821	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742989	0.90[EUR][1000 genomes]
rs12743200	0.88[EUR][1000 genomes]
rs12745610	0.96[EUR][1000 genomes]
rs12747286	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751161	0.92[EUR][1000 genomes]
rs12754832	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755338	0.85[EUR][1000 genomes]
rs12755816	0.96[EUR][1000 genomes]
rs12758302	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758579	0.88[EUR][1000 genomes]
rs12759275	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539207	0.96[EUR][1000 genomes]
rs1544196	0.87[EUR][1000 genomes]
rs16848365	0.88[EUR][1000 genomes]
rs17503938	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2185684	0.88[EUR][1000 genomes]
rs28434172	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2897048	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35011635	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031726	0.96[EUR][1000 genomes]
rs35067427	0.88[EUR][1000 genomes]
rs35169600	0.94[EUR][1000 genomes]
rs35277713	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35303987	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35341841	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35365551	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571080	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35767322	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35804313	0.83[AMR][1000 genomes]
rs35915186	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35972228	0.93[EUR][1000 genomes]
rs36138926	0.96[EUR][1000 genomes]
rs4653587	0.91[EUR][1000 genomes]
rs4654037	0.96[EUR][1000 genomes]
rs55730749	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56223447	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426121	0.99[EUR][1000 genomes]
rs6426123	0.91[EUR][1000 genomes]
rs6426125	0.91[EUR][1000 genomes]
rs6426126	0.91[EUR][1000 genomes]
rs66467176	0.88[EUR][1000 genomes]
rs6663522	0.88[EUR][1000 genomes]
rs6671751	0.94[EUR][1000 genomes]
rs6672859	0.96[EUR][1000 genomes]
rs6675858	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6691779	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693287	0.95[EUR][1000 genomes]
rs6701145	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67065875	0.94[EUR][1000 genomes]
rs68037178	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71644786	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7365151	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7512431	0.96[EUR][1000 genomes]
rs7513208	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7514284	0.99[EUR][1000 genomes]
rs7514575	0.89[EUR][1000 genomes]
rs7517754	0.94[EUR][1000 genomes]
rs7518109	0.96[EUR][1000 genomes]
rs7519734	0.94[EUR][1000 genomes]
rs7522956	0.96[EUR][1000 genomes]
rs7527044	0.92[EUR][1000 genomes]
rs7529067	0.94[EUR][1000 genomes]
rs7529310	0.91[EUR][1000 genomes]
rs867362	0.88[EUR][1000 genomes]
rs885606	0.88[EUR][1000 genomes]
rs9970697	0.87[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
rs12731035	CNIH4	cis	Thyroid	GTEx
rs12731035	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs12731035	CNIH4	cis	Esophagus Muscularis	GTEx
rs12731035	CNIH4	cis	Muscle Skeletal	GTEx
rs12731035	CNIH4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 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	chr1:224563000-224593400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224571000-224594000	Strong transcription	HMEC	breast
6	chr1:224571200-224599400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:224571800-224593400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:224572000-224594000	Strong transcription	Osteobl	bone
9	chr1:224572000-224617800	Strong transcription	Fetal Thymus	thymus
10	chr1:224572400-224601000	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:224572400-224617600	Strong transcription	Placenta	Placenta
12	chr1:224572600-224593600	Strong transcription	NHDF-Ad	bronchial
13	chr1:224572600-224593800	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:224572600-224594000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:224572600-224617600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:224572600-224617600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:224572600-224618400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:224572800-224594400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:224573200-224593400	Strong transcription	HUVEC	blood vessel
20	chr1:224573200-224594000	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr1:224573200-224594000	Strong transcription	NH-A	brain
22	chr1:224573200-224594600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:224573200-224618400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:224573200-224618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:224573600-224614200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:224573600-224618200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:224573800-224615200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:224574000-224595800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:224574000-224599400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:224574000-224601600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr1:224574000-224613600	Strong transcription	Adipose Nuclei	Adipose
32	chr1:224574200-224594400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:224574600-224613600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr1:224575000-224597200	Strong transcription	GM12878-XiMat	blood
35	chr1:224575000-224607600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:224575200-224594800	Strong transcription	Fetal Lung	lung
37	chr1:224575200-224607600	Strong transcription	Fetal Intestine Large	intestine
38	chr1:224575200-224613800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:224575200-224616600	Strong transcription	Dnd41	blood
40	chr1:224575200-224616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:224575400-224593400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:224576000-224595600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:224576000-224597200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr1:224576000-224601200	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr1:224576200-224594000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:224576200-224614000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:224576400-224614600	Strong transcription	HSMM	muscle
48	chr1:224577000-224617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:224577400-224594200	Strong transcription	Primary T cells from cord blood	blood
50	chr1:224578800-224614000	Strong transcription	Primary neutrophils fromperipheralblood	blood

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