Variant report

Variant	rs12504375
Chromosome Location	chr4:143456800-143456801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143390775..143397216-chr4:143452311..143461627,17	MCF-7	breast:
2	chr4:143444200..143447177-chr4:143456596..143458956,2	MCF-7	breast:
3	chr4:143436540..143438888-chr4:143456433..143458379,2	MCF-7	breast:
4	chr4:143454704..143456916-chr4:143459367..143461134,2	K562	blood:
5	chr4:143455514..143457916-chr4:143469730..143472176,3	MCF-7	breast:
6	chr4:143393069..143398763-chr4:143454567..143462510,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10519649	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11100748	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100749	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1160379	0.83[ASN][1000 genomes]
rs11930912	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11939291	0.81[ASN][1000 genomes]
rs11943687	0.81[ASN][1000 genomes]
rs12504378	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504770	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1425518	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1425519	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1476122	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1559709	0.81[ASN][1000 genomes]
rs16998558	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17016344	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17016354	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17717651	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2059510	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2059511	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2059513	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2217016	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34007357	0.83[ASN][1000 genomes]
rs35854467	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4246729	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4524461	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4975306	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4975313	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4975316	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975318	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58078405	0.81[ASN][1000 genomes]
rs58899027	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59732892	0.81[ASN][1000 genomes]
rs60329859	0.85[AMR][1000 genomes]
rs60951295	0.81[ASN][1000 genomes]
rs61104737	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61142249	0.80[ASN][1000 genomes]
rs6537109	0.85[EUR][1000 genomes]
rs6537110	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67900719	0.81[ASN][1000 genomes]
rs6816875	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7671198	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs890191	0.81[ASN][1000 genomes]
rs890192	0.81[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	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv461660	chr4:143437219-143538179	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv595605	chr4:143437219-143538179	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143438800-143462800	Weak transcription	Aorta	Aorta
2	chr4:143444800-143468400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:143452800-143458800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:143453000-143464000	Weak transcription	Fetal Intestine Small	intestine
5	chr4:143453600-143457000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:143453800-143458000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:143453800-143459200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:143454600-143459200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:143455400-143457000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:143456000-143456800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr4:143456000-143457000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:143456200-143456800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:143456200-143456800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:143456400-143456800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr4:143456400-143456800	Enhancers	A549	lung
16	chr4:143456400-143456800	Enhancers	HMEC	breast
17	chr4:143456800-143460400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr4:143456800-143461400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:143456800-143468400	Weak transcription	HMEC	breast

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