Variant report

Variant	rs11584247
Chromosome Location	chr1:224556098-224556099
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224552027..224554315-chr1:224555150..224556880,2	K562	blood:
2	chr1:224543261..224548633-chr1:224550034..224557593,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10127813	0.96[EUR][1000 genomes]
rs10127953	0.96[EUR][1000 genomes]
rs10128058	0.96[EUR][1000 genomes]
rs10159333	0.88[EUR][1000 genomes]
rs10495219	0.89[EUR][1000 genomes]
rs10753465	0.96[EUR][1000 genomes]
rs10753466	0.96[EUR][1000 genomes]
rs10753467	0.85[EUR][1000 genomes]
rs10753468	0.85[EUR][1000 genomes]
rs10799569	0.96[EUR][1000 genomes]
rs10916606	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916607	0.95[EUR][1000 genomes]
rs10916614	0.88[EUR][1000 genomes]
rs10916616	0.88[EUR][1000 genomes]
rs10916617	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916619	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11576835	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577170	0.85[EUR][1000 genomes]
rs11577183	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579952	0.96[EUR][1000 genomes]
rs11584638	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584980	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11586729	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11588973	0.84[EUR][1000 genomes]
rs11590658	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11800613	0.85[EUR][1000 genomes]
rs11801436	0.93[EUR][1000 genomes]
rs11801645	0.93[EUR][1000 genomes]
rs11803414	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11803981	0.96[EUR][1000 genomes]
rs11805973	0.84[EUR][1000 genomes]
rs11807763	0.86[EUR][1000 genomes]
rs11807942	0.95[EUR][1000 genomes]
rs11811053	0.92[EUR][1000 genomes]
rs12062871	0.84[EUR][1000 genomes]
rs12731035	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12731630	0.85[EUR][1000 genomes]
rs12738799	0.89[EUR][1000 genomes]
rs12739486	0.89[EUR][1000 genomes]
rs12740255	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742821	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742989	0.87[EUR][1000 genomes]
rs12743200	0.85[EUR][1000 genomes]
rs12745610	0.96[EUR][1000 genomes]
rs12747286	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751161	0.89[EUR][1000 genomes]
rs12754832	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755338	0.82[EUR][1000 genomes]
rs12755816	0.96[EUR][1000 genomes]
rs12758302	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758579	0.85[EUR][1000 genomes]
rs12759275	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539207	0.96[EUR][1000 genomes]
rs1544196	0.84[EUR][1000 genomes]
rs16848365	0.85[EUR][1000 genomes]
rs17503938	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2185684	0.85[EUR][1000 genomes]
rs28434172	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2897048	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35011635	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35031726	0.96[EUR][1000 genomes]
rs35067427	0.85[EUR][1000 genomes]
rs35169600	0.94[EUR][1000 genomes]
rs35277713	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35303987	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35341841	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[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];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35915186	0.80[EUR][1000 genomes]
rs35972228	0.92[EUR][1000 genomes]
rs36138926	0.96[EUR][1000 genomes]
rs4653587	0.88[EUR][1000 genomes]
rs4654037	0.96[EUR][1000 genomes]
rs55730749	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56223447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6426121	0.93[EUR][1000 genomes]
rs6426123	0.88[EUR][1000 genomes]
rs6426125	0.88[EUR][1000 genomes]
rs6426126	0.88[EUR][1000 genomes]
rs66467176	0.84[EUR][1000 genomes]
rs6663522	0.85[EUR][1000 genomes]
rs6671751	0.96[EUR][1000 genomes]
rs6672859	0.96[EUR][1000 genomes]
rs6675858	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6691779	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693287	0.94[EUR][1000 genomes]
rs6701145	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67065875	0.96[EUR][1000 genomes]
rs68037178	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71644786	0.84[AMR][1000 genomes]
rs7365151	0.84[EUR][1000 genomes]
rs7512431	0.96[EUR][1000 genomes]
rs7513208	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7514284	0.93[EUR][1000 genomes]
rs7514575	0.86[EUR][1000 genomes]
rs7517754	0.96[EUR][1000 genomes]
rs7518109	0.96[EUR][1000 genomes]
rs7519734	0.96[EUR][1000 genomes]
rs7522956	0.96[EUR][1000 genomes]
rs7527044	0.90[EUR][1000 genomes]
rs7529067	0.96[EUR][1000 genomes]
rs7529310	0.88[EUR][1000 genomes]
rs867362	0.85[EUR][1000 genomes]
rs885606	0.85[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11584247	CNIH4	cis	Thyroid	GTEx
rs11584247	CNIH4	cis	Muscle Skeletal	GTEx
rs11584247	CNIH4	cis	Esophagus Muscularis	GTEx
rs11584247	CNIH4	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545400-224559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
4	chr1:224546000-224556400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:224546800-224558000	Weak transcription	NHLF	lung
8	chr1:224546800-224562200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
10	chr1:224547400-224561800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:224547800-224556400	Weak transcription	Right Atrium	heart
13	chr1:224547800-224562800	Weak transcription	Pancreas	Pancrea
14	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
16	chr1:224550400-224568000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:224550800-224564200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:224550800-224565000	Strong transcription	HUVEC	blood vessel
19	chr1:224551000-224568000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:224551200-224560000	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:224551200-224563600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:224551200-224565800	Strong transcription	Primary B cells from cord blood	blood
23	chr1:224551400-224561000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:224551400-224561400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:224551400-224568600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:224551600-224560800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr1:224551600-224566600	Strong transcription	Dnd41	blood
28	chr1:224551600-224568000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:224551600-224568400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:224551800-224561600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:224552000-224561000	Strong transcription	Primary T cells from cord blood	blood
32	chr1:224552000-224564800	Weak transcription	Psoas Muscle	Psoas
33	chr1:224552600-224563800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:224552800-224562000	Strong transcription	Osteobl	bone
35	chr1:224552800-224564200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr1:224552800-224565800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:224553000-224561000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:224553000-224562800	Strong transcription	Fetal Thymus	thymus
39	chr1:224553000-224562800	Strong transcription	HSMM	muscle
40	chr1:224553000-224564200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:224553000-224565000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:224553000-224565200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:224553200-224562400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:224553200-224562800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:224553200-224564400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:224553200-224567400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:224553400-224560800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:224553400-224561200	Strong transcription	HMEC	breast
49	chr1:224553400-224562200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:224553400-224562400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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