Variant report

Variant	rs28434172
Chromosome Location	chr1:224614625-224614626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224613670..224615210-chr1:224641405..224643090,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10127813	0.88[EUR][1000 genomes]
rs10127953	0.88[EUR][1000 genomes]
rs10128058	0.88[EUR][1000 genomes]
rs10159333	0.96[EUR][1000 genomes]
rs10495219	0.98[EUR][1000 genomes]
rs10753465	0.88[EUR][1000 genomes]
rs10753466	0.88[EUR][1000 genomes]
rs10753467	0.94[EUR][1000 genomes]
rs10753468	0.94[EUR][1000 genomes]
rs10799569	0.88[EUR][1000 genomes]
rs10916606	0.87[EUR][1000 genomes]
rs10916607	0.87[EUR][1000 genomes]
rs10916614	0.97[EUR][1000 genomes]
rs10916616	0.96[EUR][1000 genomes]
rs10916617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10916619	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11576835	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11577170	0.94[EUR][1000 genomes]
rs11577183	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11578709	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11579952	0.88[EUR][1000 genomes]
rs11584057	0.81[EUR][1000 genomes]
rs11584247	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11584638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11584980	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11586729	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11588973	0.94[EUR][1000 genomes]
rs11590658	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11800613	0.94[EUR][1000 genomes]
rs11801436	0.91[EUR][1000 genomes]
rs11801645	0.91[EUR][1000 genomes]
rs11803414	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11803981	0.88[EUR][1000 genomes]
rs11805973	0.92[EUR][1000 genomes]
rs11807763	0.95[EUR][1000 genomes]
rs11807942	0.88[EUR][1000 genomes]
rs11811053	0.84[EUR][1000 genomes]
rs12062871	0.92[EUR][1000 genomes]
rs12731035	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12731630	0.94[EUR][1000 genomes]
rs12738799	0.98[EUR][1000 genomes]
rs12739486	0.98[EUR][1000 genomes]
rs12740255	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12742821	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12742989	0.96[EUR][1000 genomes]
rs12743200	0.94[EUR][1000 genomes]
rs12745610	0.88[EUR][1000 genomes]
rs12747286	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12751161	0.98[EUR][1000 genomes]
rs12754832	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12755338	0.90[EUR][1000 genomes]
rs12755816	0.88[EUR][1000 genomes]
rs12758302	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12758579	0.94[EUR][1000 genomes]
rs12759275	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1539207	0.88[EUR][1000 genomes]
rs1544196	0.92[EUR][1000 genomes]
rs16848365	0.94[EUR][1000 genomes]
rs17503938	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17570292	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2185684	0.94[EUR][1000 genomes]
rs2897048	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35011635	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35031726	0.88[EUR][1000 genomes]
rs35067427	0.94[EUR][1000 genomes]
rs35169600	0.86[EUR][1000 genomes]
rs35277713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35303987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35341841	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35365551	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35571080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35767322	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35804313	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35915186	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35972228	0.85[EUR][1000 genomes]
rs36138926	0.88[EUR][1000 genomes]
rs4653587	0.96[EUR][1000 genomes]
rs4654037	0.88[EUR][1000 genomes]
rs55730749	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56223447	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6426121	0.91[EUR][1000 genomes]
rs6426123	0.96[EUR][1000 genomes]
rs6426125	0.96[EUR][1000 genomes]
rs6426126	0.96[EUR][1000 genomes]
rs66467176	0.93[EUR][1000 genomes]
rs6663522	0.94[EUR][1000 genomes]
rs6671751	0.88[EUR][1000 genomes]
rs6672859	0.88[EUR][1000 genomes]
rs6675858	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6691779	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6693287	0.87[EUR][1000 genomes]
rs6698343	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6701145	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67065875	0.88[EUR][1000 genomes]
rs68037178	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71644786	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7365151	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7512431	0.88[EUR][1000 genomes]
rs7513208	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7514284	0.91[EUR][1000 genomes]
rs7514575	0.94[EUR][1000 genomes]
rs7517754	0.88[EUR][1000 genomes]
rs7518109	0.88[EUR][1000 genomes]
rs7519734	0.88[EUR][1000 genomes]
rs7522956	0.88[EUR][1000 genomes]
rs7527044	0.97[EUR][1000 genomes]
rs7529067	0.88[EUR][1000 genomes]
rs7529310	0.96[EUR][1000 genomes]
rs867362	0.94[EUR][1000 genomes]
rs885606	0.94[EUR][1000 genomes]
rs9970697	0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28434172	CNIH4	cis	Esophagus Muscularis	GTEx
rs28434172	CNIH4	cis	Muscle Skeletal	GTEx
rs28434172	CNIH4	cis	Thyroid	GTEx
rs28434172	CNIH4	cis	Heart Left Ventricle	GTEx
rs28434172	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:224572000-224617800	Strong transcription	Fetal Thymus	thymus
3	chr1:224572400-224617600	Strong transcription	Placenta	Placenta
4	chr1:224572600-224617600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224572600-224617600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:224572600-224618400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:224573200-224618400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:224573200-224618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:224573600-224618200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:224573800-224615200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr1:224575200-224616600	Strong transcription	Dnd41	blood
12	chr1:224575200-224616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:224577000-224617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:224578800-224617200	Strong transcription	Liver	Liver
15	chr1:224579600-224617400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:224579800-224616000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:224581800-224615800	Strong transcription	K562	blood
18	chr1:224593400-224617000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:224595400-224618000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:224596200-224615400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:224597600-224616200	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:224598200-224617000	Strong transcription	Fetal Muscle Leg	muscle
23	chr1:224599800-224618000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:224600200-224617400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:224602200-224616400	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr1:224603600-224615200	Strong transcription	A549	lung
27	chr1:224605200-224618400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:224608200-224615000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:224608400-224620800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:224609600-224618400	Weak transcription	Right Atrium	heart
31	chr1:224610000-224615000	Weak transcription	Brain Angular Gyrus	brain
32	chr1:224610000-224616600	Weak transcription	Psoas Muscle	Psoas
33	chr1:224611200-224616200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:224611800-224615200	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:224612000-224614800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:224612000-224617400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:224612000-224618400	Weak transcription	Fetal Heart	heart
38	chr1:224612000-224619400	Weak transcription	Stomach Mucosa	stomach
39	chr1:224612200-224617200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:224612200-224617400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
41	chr1:224612200-224619200	Weak transcription	Brain Germinal Matrix	brain
42	chr1:224612400-224615000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:224612400-224615000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:224612400-224615000	Weak transcription	Small Intestine	intestine
45	chr1:224612400-224615200	Weak transcription	Brain Anterior Caudate	brain
46	chr1:224612400-224615200	Weak transcription	Brain Substantia Nigra	brain
47	chr1:224612400-224616200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:224612400-224616200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:224612400-224616200	Weak transcription	Lung	lung
50	chr1:224612400-224616400	Weak transcription	Left Ventricle	heart

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