Variant report

Variant	rs11803414
Chromosome Location	chr1:224554729-224554730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224543261..224548633-chr1:224550034..224557593,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10127813	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs10127953	0.98[EUR][1000 genomes]
rs10128058	0.98[EUR][1000 genomes]
rs10159333	0.90[EUR][1000 genomes]
rs10495219	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10753465	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs10753466	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs10753467	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10753468	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs10799569	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916606	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10916607	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs10916614	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916616	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916617	0.94[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916619	0.94[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11576835	0.95[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11577170	0.87[EUR][1000 genomes]
rs11577183	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11579952	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584247	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11584980	0.89[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11586729	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11588973	0.86[EUR][1000 genomes]
rs11590658	0.94[CEU][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11800613	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs11801436	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11803981	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805973	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs11807763	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs11807942	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811053	0.94[EUR][1000 genomes]
rs12062871	0.86[EUR][1000 genomes]
rs12731035	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12731630	0.87[EUR][1000 genomes]
rs12738799	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12739486	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12740255	0.89[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12742821	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12742989	0.89[EUR][1000 genomes]
rs12743200	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12745610	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs12747286	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12751161	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12755338	0.83[EUR][1000 genomes]
rs12755816	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs12758302	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12758579	0.87[EUR][1000 genomes]
rs12759275	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1539207	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs1544196	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs16848365	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs17503938	0.94[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185684	0.87[EUR][1000 genomes]
rs28434172	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2897048	0.94[CEU][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35011635	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35031726	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067427	0.87[EUR][1000 genomes]
rs35169600	0.96[EUR][1000 genomes]
rs35277713	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35303987	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35341841	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35365551	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35571080	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35915186	0.82[EUR][1000 genomes]
rs35972228	0.94[EUR][1000 genomes]
rs36138926	0.98[EUR][1000 genomes]
rs4653585	0.94[CEU][hapmap]
rs4653587	0.90[EUR][1000 genomes]
rs4654037	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs55730749	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56223447	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6426121	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs6426123	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs6426125	0.90[EUR][1000 genomes]
rs6426126	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs66467176	0.86[EUR][1000 genomes]
rs6663522	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6671751	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672859	0.98[EUR][1000 genomes]
rs6675858	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691779	0.89[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6693287	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs6701145	0.94[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67065875	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68037178	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71644786	0.84[AMR][1000 genomes]
rs7365151	0.86[EUR][1000 genomes]
rs7512431	0.98[EUR][1000 genomes]
rs7513208	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514284	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs7514575	0.87[EUR][1000 genomes]
rs7517754	0.94[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518109	0.98[EUR][1000 genomes]
rs7519734	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522956	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs7527044	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7529067	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529310	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs867362	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs885606	0.87[EUR][1000 genomes]
rs9970697	0.86[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
rs11803414	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs11803414	CNIH4	cis	Thyroid	GTEx
rs11803414	CNIH4	cis	Heart Left Ventricle	GTEx
rs11803414	CNIH4	cis	Muscle Skeletal	GTEx
rs11803414	CNIH4	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545200-224555200	Weak transcription	Spleen	Spleen
2	chr1:224545400-224559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224545600-224555200	Weak transcription	Lung	lung
4	chr1:224545600-224555200	Weak transcription	Ovary	ovary
5	chr1:224545800-224555000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
8	chr1:224546000-224555200	Weak transcription	Fetal Kidney	kidney
9	chr1:224546000-224556400	Weak transcription	Brain Angular Gyrus	brain
10	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:224546200-224554800	Weak transcription	Placenta	Placenta
13	chr1:224546200-224554800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:224546200-224555200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:224546200-224555200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:224546200-224555200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:224546200-224555200	Weak transcription	Colonic Mucosa	Colon
18	chr1:224546200-224555200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:224546200-224555200	Weak transcription	Right Ventricle	heart
20	chr1:224546200-224555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:224546400-224555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:224546400-224555200	Weak transcription	Left Ventricle	heart
23	chr1:224546400-224555400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:224546800-224554800	Weak transcription	Hela-S3	cervix
25	chr1:224546800-224555200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:224546800-224558000	Weak transcription	NHLF	lung
27	chr1:224546800-224562200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:224547000-224554800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:224547000-224554800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:224547000-224555200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:224547000-224555200	Weak transcription	Brain Germinal Matrix	brain
32	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
33	chr1:224547200-224555000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:224547200-224555400	Weak transcription	Fetal Heart	heart
35	chr1:224547400-224554800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:224547400-224561800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:224547600-224555200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:224547800-224555200	Weak transcription	Esophagus	oesophagus
40	chr1:224547800-224555200	Weak transcription	Gastric	stomach
41	chr1:224547800-224556400	Weak transcription	Right Atrium	heart
42	chr1:224547800-224562800	Weak transcription	Pancreas	Pancrea
43	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:224548000-224554800	Weak transcription	Fetal Brain Female	brain
45	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
46	chr1:224548600-224554800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:224548800-224555000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:224549800-224554800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:224549800-224555400	Weak transcription	K562	blood
50	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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