Variant report

Variant	rs11801645
Chromosome Location	chr1:224597216-224597217
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224596374..224598297-chr1:224606447..224608746,2	MCF-7	breast:
2	chr1:224592543..224595512-chr1:224595755..224597516,2	K562	blood:
3	chr1:224595603..224601847-chr1:224621020..224623770,7	MCF-7	breast:
4	chr1:224591069..224594043-chr1:224595295..224597255,3	K562	blood:
5	chr1:224595604..224598812-chr1:224605790..224608888,3	MCF-7	breast:
6	chr1:224595735..224597689-chr1:224599176..224602327,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162923	Chromatin interaction
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10127813	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127953	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128058	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10159333	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495219	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753465	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753467	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753468	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10799569	0.97[EUR][1000 genomes]
rs10916606	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916616	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916617	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10916619	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11576835	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11577170	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11577183	0.96[EUR][1000 genomes]
rs11579952	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11584247	0.93[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11584980	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs11586729	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11588973	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11590658	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11800613	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11801436	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803414	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11803981	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11805973	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807763	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807942	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11811053	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12062871	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12731035	0.99[EUR][1000 genomes]
rs12731630	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12738799	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740255	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs12742821	0.96[EUR][1000 genomes]
rs12742989	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12743200	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12745610	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12747286	0.92[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs12755338	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12755816	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758302	0.86[EUR][1000 genomes]
rs12758579	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12759275	0.96[EUR][1000 genomes]
rs1539207	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848365	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503938	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs2185684	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28434172	0.91[EUR][1000 genomes]
rs2897048	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs34791963	0.84[AMR][1000 genomes]
rs35011635	0.90[EUR][1000 genomes]
rs35031726	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35067427	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35169600	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35277713	0.91[EUR][1000 genomes]
rs35303987	0.91[EUR][1000 genomes]
rs35341841	0.94[EUR][1000 genomes]
rs35365551	0.87[EUR][1000 genomes]
rs35571080	0.88[EUR][1000 genomes]
rs35767322	0.81[EUR][1000 genomes]
rs35915186	0.84[EUR][1000 genomes]
rs35972228	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36138926	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654037	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs55730749	0.88[EUR][1000 genomes]
rs56223447	0.96[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426123	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426125	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6426126	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467176	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6671751	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6672859	0.97[EUR][1000 genomes]
rs6675858	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6691779	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701145	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs67065875	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68037178	0.95[EUR][1000 genomes]
rs71644786	0.81[EUR][1000 genomes]
rs7365151	0.88[EUR][1000 genomes]
rs7512431	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513208	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7514284	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514575	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517754	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs7518109	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519734	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7522956	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529067	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7529310	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885606	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970697	0.83[AMR][1000 genomes];0.88[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
rs11801645	CNIH4	cis	Adipose Subcutaneous	GTEx
rs11801645	CNIH4	cis	Nerve Tibial	GTEx
rs11801645	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs11801645	CNIH4	cis	Muscle Skeletal	GTEx
rs11801645	CNIH4	cis	Esophagus Muscularis	GTEx
rs11801645	CNIH4	cis	Esophagus Mucosa	GTEx
rs11801645	CNIH4	cis	Stomach	GTEx
rs11801645	CNIH4	cis	Thyroid	GTEx
rs11801645	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	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:224571200-224599400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:224572000-224617800	Strong transcription	Fetal Thymus	thymus
5	chr1:224572400-224601000	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:224572400-224617600	Strong transcription	Placenta	Placenta
7	chr1:224572600-224617600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:224572600-224617600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:224572600-224618400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:224573200-224618400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:224573200-224618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:224573600-224614200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:224573600-224618200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:224573800-224615200	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr1:224574000-224599400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:224574000-224601600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:224574000-224613600	Strong transcription	Adipose Nuclei	Adipose
18	chr1:224574600-224613600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:224575000-224607600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:224575200-224607600	Strong transcription	Fetal Intestine Large	intestine
21	chr1:224575200-224613800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr1:224575200-224616600	Strong transcription	Dnd41	blood
23	chr1:224575200-224616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:224576000-224601200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:224576200-224614000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:224576400-224614600	Strong transcription	HSMM	muscle
27	chr1:224577000-224617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:224578800-224614000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:224578800-224617200	Strong transcription	Liver	Liver
30	chr1:224579600-224617400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:224579800-224616000	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr1:224581000-224599600	Strong transcription	HepG2	liver
33	chr1:224581800-224615800	Strong transcription	K562	blood
34	chr1:224583200-224604200	Weak transcription	Fetal Heart	heart
35	chr1:224584200-224599000	Strong transcription	Primary B cells from cord blood	blood
36	chr1:224585000-224599400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr1:224585600-224599000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:224587000-224600000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:224589000-224611200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:224589600-224597800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:224590400-224598000	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:224590400-224599200	Strong transcription	HSMMtube	muscle
43	chr1:224590400-224600400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:224590400-224612600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:224590800-224597600	Strong transcription	Left Ventricle	heart
46	chr1:224591200-224599200	Strong transcription	Brain Anterior Caudate	brain
47	chr1:224591200-224613000	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:224591400-224607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr1:224591600-224600600	Strong transcription	Brain Cingulate Gyrus	brain
50	chr1:224592400-224605400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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