Variant report

Variant	rs11584980
Chromosome Location	chr1:224564374-224564375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:224563977-224565178	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:224564335-224564511	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA2	chr1:224564159-224564459	SH-SY5Y	brain:	n/a	n/a
4	FOSL2	chr1:224564291-224565020	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:224564318-224565908	SK-N-SH	brain:	n/a	chr1:224565544-224565555
6	GATA3	chr1:224564129-224564472	SH-SY5Y	brain:	n/a	n/a
7	GATA3	chr1:224563932-224565224	SK-N-SH	brain:	n/a	n/a
8	NFIC	chr1:224564260-224565212	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224562792..224564765-chr1:224585546..224588270,2	K562	blood:
2	chr1:224543721..224546086-chr1:224562908..224565121,2	MCF-7	breast:

Variant related genes	Relation type
CNIH4	TF binding region
ENSG00000143771	Chromatin interaction
ENSG00000266618	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10127813	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10127953	0.99[EUR][1000 genomes]
rs10128058	0.99[EUR][1000 genomes]
rs10159333	0.88[EUR][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10753465	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10753466	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs10753467	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753468	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs10799569	0.99[EUR][1000 genomes]
rs10916606	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916607	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs10916614	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10916616	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs10916617	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916619	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577170	0.86[EUR][1000 genomes]
rs11577183	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579952	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs11584247	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584638	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586729	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11588973	0.85[EUR][1000 genomes]
rs11590658	0.94[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11801436	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11801645	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs11803414	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11803981	0.96[EUR][1000 genomes]
rs11805973	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];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];1.00[ASN][1000 genomes]
rs12731630	0.86[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12739486	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12740255	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742821	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742989	0.88[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12745610	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12747286	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12754832	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755338	0.82[EUR][1000 genomes]
rs12755816	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12758302	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758579	0.86[EUR][1000 genomes]
rs12759275	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539207	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs1544196	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs16848365	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs17503938	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35011635	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][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];1.00[ASN][1000 genomes]
rs35303987	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35341841	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35365551	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571080	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35915186	0.81[EUR][1000 genomes]
rs35972228	0.96[EUR][1000 genomes]
rs36138926	0.99[EUR][1000 genomes]
rs4653585	0.95[CEU][hapmap]
rs4653587	0.88[EUR][1000 genomes]
rs4654037	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs55730749	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56223447	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs6426123	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6426125	0.88[EUR][1000 genomes]
rs6426126	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs66467176	0.85[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6671751	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs6672859	0.99[EUR][1000 genomes]
rs6675858	0.81[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6691779	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693287	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs6701145	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67065875	0.96[EUR][1000 genomes]
rs68037178	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71644786	0.84[AMR][1000 genomes]
rs7365151	0.85[EUR][1000 genomes]
rs7512431	0.99[EUR][1000 genomes]
rs7513208	0.90[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7514284	0.86[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7514575	0.86[EUR][1000 genomes]
rs7517754	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7518109	0.99[EUR][1000 genomes]
rs7519734	0.96[EUR][1000 genomes]
rs7522956	0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs7527044	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7529067	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs7529310	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs867362	0.95[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11584980	CNIH4	cis	Muscle Skeletal	GTEx
rs11584980	CNIH4	cis	parietal	SCAN
rs11584980	CNIH4	cis	Heart Left Ventricle	GTEx
rs11584980	CNIH4	cis	Thyroid	GTEx
rs11584980	CNIH4	cis	Esophagus Muscularis	GTEx
rs11584980	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
4	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
7	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:224550800-224565000	Strong transcription	HUVEC	blood vessel
9	chr1:224551000-224568000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:224551200-224565800	Strong transcription	Primary B cells from cord blood	blood
11	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr1:224551600-224566600	Strong transcription	Dnd41	blood
13	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:224552000-224564800	Weak transcription	Psoas Muscle	Psoas
16	chr1:224552800-224565800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:224553000-224565000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:224553000-224565200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:224553200-224564400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:224553400-224565000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:224553400-224567000	Strong transcription	Adipose Nuclei	Adipose
23	chr1:224553400-224567400	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:224553600-224564400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:224553600-224566000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:224553600-224566400	Strong transcription	Fetal Intestine Small	intestine
27	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
28	chr1:224554200-224565600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:224554400-224568200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr1:224554600-224567200	Strong transcription	Liver	Liver
31	chr1:224554600-224567400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:224554800-224568600	Strong transcription	Fetal Brain Female	brain
33	chr1:224555000-224564400	Strong transcription	Stomach Smooth Muscle	stomach
34	chr1:224555000-224568000	Strong transcription	Brain Anterior Caudate	brain
35	chr1:224555000-224568200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:224555200-224564400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr1:224555200-224566000	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr1:224555200-224568000	Strong transcription	Brain Germinal Matrix	brain
39	chr1:224555400-224565400	Strong transcription	HepG2	liver
40	chr1:224555800-224581400	Weak transcription	Fetal Heart	heart
41	chr1:224556000-224591000	Weak transcription	Small Intestine	intestine
42	chr1:224558000-224564600	Strong transcription	NHLF	lung
43	chr1:224558200-224564600	Strong transcription	K562	blood
44	chr1:224558200-224567200	Strong transcription	A549	lung
45	chr1:224559000-224565000	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:224559800-224564800	Weak transcription	Right Ventricle	heart
47	chr1:224560200-224565200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:224560400-224565000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr1:224560600-224564600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr1:224560600-224564800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood

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