Variant report

Variant	rs10519649
Chromosome Location	chr4:143454553-143454554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143390775..143397216-chr4:143452311..143461627,17	MCF-7	breast:
2	chr4:143451539..143454827-chr4:143468974..143471578,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10857395	0.81[JPT][hapmap]
rs11100748	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11100749	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11728822	0.94[JPT][hapmap]
rs11930912	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11939291	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs11943687	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs12504375	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12504378	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12504418	0.88[JPT][hapmap]
rs12504770	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1425518	0.86[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1425519	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1476122	0.80[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1559709	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs16998558	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16998560	0.88[JPT][hapmap]
rs17016344	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17016354	0.80[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17717651	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059510	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059511	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059513	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2217016	0.86[CEU][hapmap];0.84[CHB][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35854467	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4246729	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4524461	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4975306	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4975313	0.83[CEU][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4975316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975317	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58899027	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60329859	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs61104737	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537109	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs6537110	0.81[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6816875	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7671198	0.83[EUR][1000 genomes];0.83[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519649	C7orf25	trans	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143438800-143462800	Weak transcription	Aorta	Aorta
2	chr4:143444400-143456400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr4:143444800-143468400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:143451400-143455400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:143452800-143458800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:143453000-143464000	Weak transcription	Fetal Intestine Small	intestine
7	chr4:143453600-143457000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:143453800-143455600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr4:143453800-143458000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:143453800-143459200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr4:143454200-143454600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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