Variant report

Variant	rs12124547
Chromosome Location	chr1:224407117-224407118
allele	A/G
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	CEBPB	chr1:224406873-224407188	K562	blood:	n/a	chr1:224407028-224407039
2	KAP1	chr1:224406716-224407544	U2OS	brain:	n/a	n/a
3	KAP1	chr1:224406659-224407655	HEK293	kidney:	n/a	n/a
4	CEBPB	chr1:224406938-224407186	HepG2	liver:	n/a	chr1:224407028-224407039
5	STAT3	chr1:224407100-224407189	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr1:224407100-224407197	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr1:224406967-224407267	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:224407007-224407207	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr1:224406915-224407209	Hela-S3	cervix:	n/a	chr1:224407028-224407039
10	CEBPB	chr1:224406941-224407185	A549	lung:	n/a	chr1:224407028-224407039
11	CEBPB	chr1:224406892-224407209	IMR90	lung:	n/a	chr1:224407028-224407039
12	STAT3	chr1:224407044-224407141	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr1:224406936-224407292	MCF10A-Er-Src	breast:	n/a	n/a
14	CEBPB	chr1:224406929-224407123	H1-hESC	embryonic stem cell:	n/a	chr1:224407028-224407039
15	CEBPB	chr1:224406911-224407196	K562	blood:	n/a	chr1:224407028-224407039

Variant related genes	Relation type
ENSG00000237101	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10799491	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10799507	0.88[EUR][1000 genomes]
rs10799543	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916458	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10916462	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916472	0.88[EUR][1000 genomes]
rs10916481	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916497	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916498	0.96[EUR][1000 genomes]
rs12082619	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12083770	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12120308	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126765	0.88[EUR][1000 genomes]
rs12126815	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12133599	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12140137	0.92[EUR][1000 genomes]
rs12184283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45583539	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.88[EUR][1000 genomes]
rs6686449	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6694451	1.00[CEU][hapmap]
rs6701036	0.81[EUR][1000 genomes]
rs68073536	0.96[EUR][1000 genomes]
rs72753956	0.88[EUR][1000 genomes]
rs72753969	0.88[EUR][1000 genomes]
rs72753980	0.80[EUR][1000 genomes]
rs72753994	0.88[EUR][1000 genomes]
rs72754000	0.92[EUR][1000 genomes]
rs72754001	0.85[EUR][1000 genomes]
rs72755905	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7514140	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7552239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12124547	CNIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224389600-224414400	Weak transcription	Fetal Brain Female	brain
2	chr1:224393800-224414200	Weak transcription	Colonic Mucosa	Colon
3	chr1:224394000-224414000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:224394000-224414600	Weak transcription	HMEC	breast
5	chr1:224398000-224414200	Weak transcription	Spleen	Spleen
6	chr1:224399400-224411000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:224399400-224414200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:224399400-224414200	Weak transcription	Brain Anterior Caudate	brain
9	chr1:224401400-224413800	Weak transcription	Primary B cells from cord blood	blood
10	chr1:224401400-224413800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:224401400-224414800	Weak transcription	Right Ventricle	heart
12	chr1:224401600-224414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:224401800-224411000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:224401800-224411000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:224401800-224411000	Weak transcription	Small Intestine	intestine
16	chr1:224401800-224415200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:224401800-224427600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:224401800-224475400	Weak transcription	Esophagus	oesophagus
19	chr1:224402200-224411000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:224402200-224413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:224402200-224414200	Weak transcription	GM12878-XiMat	blood
22	chr1:224403800-224411000	Weak transcription	Left Ventricle	heart
23	chr1:224404000-224411600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:224404400-224411200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:224405600-224407200	Enhancers	K562	blood
26	chr1:224405600-224407600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr1:224405600-224407800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:224405600-224407800	Enhancers	Fetal Kidney	kidney
29	chr1:224405600-224408000	Enhancers	Fetal Intestine Large	intestine
30	chr1:224405800-224408000	Enhancers	Fetal Intestine Small	intestine
31	chr1:224406000-224407200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:224406000-224407200	Weak transcription	HUVEC	blood vessel
33	chr1:224406000-224407600	Enhancers	Fetal Thymus	thymus
34	chr1:224406000-224414200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:224406200-224407200	Weak transcription	Fetal Lung	lung
36	chr1:224406200-224413800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:224406200-224414200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:224406200-224414200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:224406200-224414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:224406200-224414200	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:224406200-224414400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:224406400-224407600	Enhancers	Stomach Mucosa	stomach
45	chr1:224406400-224408000	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:224406400-224414200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:224406600-224407200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:224406600-224407200	Enhancers	Placenta	Placenta
49	chr1:224406600-224407400	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr1:224406600-224407400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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