Variant report

Variant	rs11805973
Chromosome Location	chr1:224619822-224619823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:224619112-224623610	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:224619737-224621163	HepG2	liver:	n/a	n/a
3	ARID3A	chr1:224619341-224619938	K562	blood:	n/a	n/a
4	POLR2A	chr1:224619091-224622080	K562	blood:	n/a	n/a
5	POLR2A	chr1:224619305-224621195	PBDE	blood:	n/a	n/a
6	ZNF384	chr1:224619480-224619914	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:224619206-224622083	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:224619066-224621596	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:224618157-224621611	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224370348..224372775-chr1:224619496..224622200,4	K562	blood:
2	chr1:224369742..224372382-chr1:224618245..224620019,2	MCF-7	breast:
3	chr1:224543329..224547108-chr1:224619239..224622996,5	MCF-7	breast:
4	chr1:224031722..224035110-chr1:224617781..224620783,3	K562	blood:
5	chr1:224543781..224546462-chr1:224616960..224621011,5	K562	blood:

No data

Variant related genes	Relation type
CNIH3	TF binding region
ENSG00000143771	Chromatin interaction
ENSG00000143514	Chromatin interaction
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10127813	0.95[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10127953	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10128058	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10159333	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753465	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10753466	0.95[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753467	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753468	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10799569	0.85[EUR][1000 genomes]
rs10916606	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10916607	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs10916614	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916616	0.95[CEU][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916617	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs10916619	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11577170	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11577183	0.84[EUR][1000 genomes]
rs11578709	0.83[EUR][1000 genomes]
rs11579952	0.91[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11584057	0.81[EUR][1000 genomes]
rs11584247	0.84[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11584980	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs11586729	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11588973	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11590658	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11801436	0.95[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801645	0.95[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803414	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11803981	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807942	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11811053	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12062871	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12731035	0.87[EUR][1000 genomes]
rs12731630	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739486	0.95[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740255	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs12742821	0.84[EUR][1000 genomes]
rs12742989	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12745610	0.95[CEU][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12747286	0.92[EUR][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs12755338	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12755816	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758302	0.90[EUR][1000 genomes]
rs12758579	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12759275	0.84[EUR][1000 genomes]
rs1539207	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1544196	0.95[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848365	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503938	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs17570292	0.82[EUR][1000 genomes]
rs2185684	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28434172	0.92[EUR][1000 genomes]
rs2897048	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs34791963	0.87[AMR][1000 genomes]
rs35011635	0.96[EUR][1000 genomes]
rs35031726	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35067427	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35169600	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35277713	0.95[EUR][1000 genomes]
rs35303987	0.95[EUR][1000 genomes]
rs35341841	0.81[EUR][1000 genomes]
rs35365551	0.91[EUR][1000 genomes]
rs35571080	0.92[EUR][1000 genomes]
rs35767322	0.85[EUR][1000 genomes]
rs35804313	0.83[EUR][1000 genomes]
rs35915186	0.88[EUR][1000 genomes]
rs35972228	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36138926	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4653585	0.95[CEU][hapmap]
rs4653587	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654037	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs55730749	0.92[EUR][1000 genomes]
rs56223447	0.84[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426123	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426125	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426126	0.95[CEU][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467176	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6671751	0.91[CEU][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6672859	0.85[EUR][1000 genomes]
rs6675858	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs6691779	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6693287	0.95[CEU][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs6698343	0.82[EUR][1000 genomes]
rs6701145	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs67065875	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68037178	0.83[EUR][1000 genomes]
rs71644786	0.85[EUR][1000 genomes]
rs7365151	0.92[EUR][1000 genomes]
rs7512431	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513208	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7514284	0.86[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514575	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517754	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs7518109	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519734	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7522956	0.95[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527044	0.95[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529067	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7529310	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885606	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970697	0.86[AMR][1000 genomes];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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11805973	CNIH4	cis	Adipose Subcutaneous	GTEx
rs11805973	CNIH4	cis	Stomach	GTEx
rs11805973	CNIH4	cis	Muscle Skeletal	GTEx
rs11805973	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs11805973	CNIH4	cis	Thyroid	GTEx
rs11805973	CNIH4	cis	Esophagus Mucosa	GTEx
rs11805973	CNIH4	cis	Nerve Tibial	GTEx
rs11805973	CNIH4	cis	Heart Left Ventricle	GTEx
rs11805973	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224608400-224620800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:224612400-224620000	Weak transcription	Ovary	ovary
3	chr1:224612400-224620400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224612400-224620400	Weak transcription	Esophagus	oesophagus
5	chr1:224612400-224620400	Weak transcription	Pancreas	Pancrea
6	chr1:224612400-224620600	Weak transcription	Spleen	Spleen
7	chr1:224613000-224620400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:224613000-224620400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:224616800-224620200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:224616800-224620800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:224617000-224620400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:224617000-224620400	Weak transcription	Gastric	stomach
13	chr1:224617000-224620400	Weak transcription	Lung	lung
14	chr1:224617200-224620200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:224617600-224620000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:224617600-224621000	Transcr. at gene 5' and 3'	K562	blood
17	chr1:224617600-224621200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:224617800-224621000	Flanking Active TSS	HUVEC	blood vessel
19	chr1:224618000-224620600	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:224618000-224621200	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr1:224618400-224620000	Enhancers	Fetal Heart	heart
22	chr1:224618400-224620800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
23	chr1:224618400-224621000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
24	chr1:224618400-224621000	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr1:224618400-224622800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:224618400-224623400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:224618400-224623400	Active TSS	Right Atrium	heart
28	chr1:224618400-224623600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:224618600-224620400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:224618600-224621200	Flanking Active TSS	Liver	Liver
31	chr1:224618600-224623400	Active TSS	Aorta	Aorta
32	chr1:224618800-224620000	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:224618800-224620000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:224618800-224620400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:224618800-224621000	Transcr. at gene 5' and 3'	A549	lung
36	chr1:224618800-224621800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:224618800-224622800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:224618800-224623000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:224619000-224620800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr1:224619200-224620200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:224619200-224620200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr1:224619200-224620200	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr1:224619200-224620600	Transcr. at gene 5' and 3'	Osteobl	bone
44	chr1:224619200-224620800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
45	chr1:224619200-224620800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
46	chr1:224619200-224620800	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr1:224619200-224620800	Transcr. at gene 5' and 3'	Dnd41	blood
48	chr1:224619200-224621000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr1:224619200-224621000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:224619200-224621200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell

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