Variant report

Variant	rs12498415
Chromosome Location	chr4:76558024-76558025
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76438650..76441575-chr4:76556052..76558649,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174796	Chromatin interaction
ENSG00000163743	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10856853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097121	1.00[JPT][hapmap]
rs11556146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723767	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs11734358	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11935073	1.00[JPT][hapmap]
rs12511575	1.00[JPT][hapmap]
rs16996019	0.92[JPT][hapmap]
rs17000786	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17000794	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17000864	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17215400	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17280714	0.89[EUR][1000 genomes]
rs2089253	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs324686	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324690	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs324693	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324703	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324714	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324719	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324723	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324726	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324727	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324733	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324735	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs324740	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4262008	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4610362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs60225400	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60945555	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6531816	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6531934	1.00[JPT][hapmap]
rs6816990	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850797	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6851487	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6856162	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7663617	1.00[JPT][hapmap]

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	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv1793652	chr4:76521217-76581775	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12498415	CXCL10	cis	parietal	SCAN
rs12498415	SCARB2	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76556200-76559200	Weak transcription	HSMM	muscle
2	chr4:76556200-76567600	Weak transcription	Liver	Liver
3	chr4:76556200-76590000	Weak transcription	Small Intestine	intestine
4	chr4:76556400-76558200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:76556400-76558600	Weak transcription	HMEC	breast
6	chr4:76556400-76559600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr4:76556400-76562200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:76556400-76562400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:76556400-76562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:76556400-76562800	Weak transcription	Aorta	Aorta
11	chr4:76556400-76565000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:76556400-76565200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:76556400-76565200	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:76556400-76565600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:76556400-76565600	Weak transcription	Fetal Stomach	stomach
16	chr4:76556400-76567000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:76556400-76567400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:76556400-76567400	Weak transcription	Placenta	Placenta
19	chr4:76556400-76567400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:76556400-76567800	Weak transcription	NHDF-Ad	bronchial
21	chr4:76556400-76568000	Weak transcription	Primary B cells from cord blood	blood
22	chr4:76556400-76568000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:76556400-76568000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:76556400-76568200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:76556400-76568600	Weak transcription	Adipose Nuclei	Adipose
26	chr4:76556400-76568600	Weak transcription	GM12878-XiMat	blood
27	chr4:76556400-76568600	Weak transcription	HUVEC	blood vessel
28	chr4:76556400-76568600	Weak transcription	Osteobl	bone
29	chr4:76556400-76568800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:76556400-76568800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr4:76556400-76568800	Weak transcription	Thymus	Thymus
32	chr4:76556400-76568800	Weak transcription	NH-A	brain
33	chr4:76556400-76569000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr4:76556400-76569000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:76556400-76569000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:76556400-76569000	Weak transcription	Stomach Mucosa	stomach
37	chr4:76556400-76569800	Weak transcription	Psoas Muscle	Psoas
38	chr4:76556400-76570000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:76556400-76570000	Weak transcription	Fetal Brain Male	brain
40	chr4:76556400-76570200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr4:76556400-76570600	Weak transcription	Esophagus	oesophagus
42	chr4:76556400-76570600	Weak transcription	Lung	lung
43	chr4:76556400-76570600	Weak transcription	Ovary	ovary
44	chr4:76556400-76570600	Weak transcription	Spleen	Spleen
45	chr4:76556600-76559600	Weak transcription	NHEK	skin
46	chr4:76556600-76560800	Weak transcription	Fetal Kidney	kidney
47	chr4:76556600-76562600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:76556600-76562800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:76556600-76565200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:76556600-76565600	Weak transcription	Fetal Thymus	thymus

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