Variant report

Variant	rs12504328
Chromosome Location	chr4:8453663-8453664
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	CEBPB	chr4:8453211-8453680	K562	blood:	n/a	chr4:8453458-8453471 chr4:8453626-8453639 chr4:8453459-8453470 chr4:8453458-8453469
2	POLR2A	chr4:8452932-8453846	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr4:8453215-8453767	K562	blood:	n/a	chr4:8453458-8453471 chr4:8453626-8453639 chr4:8453459-8453470 chr4:8453458-8453469

No.	Distal block	Cell Line	Cell type
1	chr4:8451516..8453879-chr4:8455754..8457384,2	MCF-7	breast:
2	chr4:8451706..8454826-chr4:8468396..8471846,3	K562	blood:
3	chr4:8448973..8451278-chr4:8451762..8453729,2	K562	blood:
4	chr4:8442272..8444111-chr4:8452996..8454572,2	MCF-7	breast:

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000087008	Chromatin interaction
ENSG00000251186	Chromatin interaction
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10003554	1.00[ASN][1000 genomes]
rs10516192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[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];1.00[ASN][1000 genomes]
rs11933361	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938744	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12108233	0.89[EUR][1000 genomes]
rs12108264	0.89[EUR][1000 genomes]
rs12108299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498220	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12498652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12498856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12499366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs12500106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500186	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500188	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.81[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];1.00[ASN][1000 genomes]
rs12501889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503080	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12504709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12504813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506061	1.00[ASN][1000 genomes]
rs12506272	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506429	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]
rs12506703	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509044	1.00[ASN][1000 genomes]
rs12509545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512044	1.00[ASN][1000 genomes]
rs12513048	1.00[ASN][1000 genomes]
rs12513296	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][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];1.00[ASN][1000 genomes]
rs16842315	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842333	1.00[CHB][hapmap]
rs2386224	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2386225	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34873641	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41264711	1.00[ASN][1000 genomes]
rs55856487	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57229672	1.00[ASN][1000 genomes]
rs59670959	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59872851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62286004	1.00[ASN][1000 genomes]
rs6447869	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs66675498	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66794792	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67332046	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67496006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67901119	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813671	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814866	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6830523	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap]
rs6849528	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6855235	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs73209462	1.00[ASN][1000 genomes]
rs73209465	1.00[ASN][1000 genomes]
rs73209470	1.00[ASN][1000 genomes]
rs73209473	1.00[ASN][1000 genomes]
rs73209478	1.00[ASN][1000 genomes]
rs73209480	1.00[ASN][1000 genomes]
rs73209481	1.00[ASN][1000 genomes]
rs73209488	1.00[ASN][1000 genomes]
rs73209489	1.00[ASN][1000 genomes]
rs73209502	1.00[ASN][1000 genomes]
rs73211306	1.00[ASN][1000 genomes]
rs73211309	1.00[ASN][1000 genomes]
rs73211315	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211334	1.00[ASN][1000 genomes]
rs73211338	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211340	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211347	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211351	0.89[EUR][1000 genomes]
rs73211354	0.89[EUR][1000 genomes]
rs73211357	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211359	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211365	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211366	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211368	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211373	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211375	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211378	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211381	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211383	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211388	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73211394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73211401	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213406	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213409	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213413	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73213420	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73213426	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223242	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223246	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223250	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223256	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223257	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223259	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223263	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223264	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223266	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223271	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223275	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223282	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73223294	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747579	1.00[CHD][hapmap]
rs7686550	1.00[ASN][1000 genomes]
rs9761200	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv461220	chr4:8372944-8458394	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv593638	chr4:8372944-8458394	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8443600-8455400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:8444200-8456800	Weak transcription	A549	lung
3	chr4:8444400-8455400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:8444600-8455800	Weak transcription	NHDF-Ad	bronchial
5	chr4:8444800-8458400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:8445000-8454600	Weak transcription	NH-A	brain
7	chr4:8445000-8454800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:8445000-8460800	Weak transcription	Psoas Muscle	Psoas
9	chr4:8445200-8454600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:8445200-8454600	Weak transcription	Small Intestine	intestine
11	chr4:8445200-8461400	Weak transcription	Hela-S3	cervix
12	chr4:8445400-8453800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr4:8445400-8455000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr4:8445600-8453800	Weak transcription	Right Atrium	heart
15	chr4:8446400-8457400	Strong transcription	Fetal Intestine Small	intestine
16	chr4:8446400-8463200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
18	chr4:8446600-8463600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:8446600-8463600	Strong transcription	Thymus	Thymus
20	chr4:8446600-8464600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:8446600-8473400	Strong transcription	Dnd41	blood
22	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
23	chr4:8446800-8456800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr4:8446800-8463800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:8447000-8458200	Strong transcription	HepG2	liver
26	chr4:8447000-8461800	Strong transcription	Fetal Intestine Large	intestine
27	chr4:8447000-8464000	Strong transcription	Primary B cells from cord blood	blood
28	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
29	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:8447200-8457400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:8447200-8458000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:8447200-8458200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:8447200-8464200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr4:8447200-8473000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:8447400-8463600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
40	chr4:8447600-8464000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:8447600-8472200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr4:8447800-8458400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:8447800-8459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:8447800-8461200	Strong transcription	Liver	Liver
46	chr4:8447800-8461800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:8447800-8463400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr4:8447800-8463400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:8447800-8463600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:8447800-8463800	Strong transcription	Brain Cingulate Gyrus	brain

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