Variant report

Variant	rs876957
Chromosome Location	chr8:61664214-61664215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:61591104..61592610-chr8:61663066..61665396,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171316	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10092214	1.00[YRI][hapmap]
rs10106752	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1017861	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1017862	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10283352	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12680437	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs13253647	1.00[YRI][hapmap]
rs13264416	0.83[AMR][1000 genomes]
rs13280978	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473446	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483208	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826359	1.00[YRI][hapmap]
rs2056415	1.00[YRI][hapmap]
rs2326569	1.00[YRI][hapmap]
rs2326570	1.00[YRI][hapmap]
rs2326571	1.00[YRI][hapmap]
rs2680297	1.00[YRI][hapmap]
rs28609390	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28710955	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946154	1.00[YRI][hapmap]
rs35168272	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35331770	0.80[AMR][1000 genomes]
rs3814483	1.00[YRI][hapmap]
rs4237036	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4288413	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4738813	0.87[CEU][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs4738816	0.87[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs4738817	0.85[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap]
rs4738826	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4738828	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4738829	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs617834	1.00[YRI][hapmap]
rs652422	1.00[YRI][hapmap]
rs671204	1.00[YRI][hapmap]
rs7011801	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7013249	1.00[YRI][hapmap]
rs7822621	1.00[YRI][hapmap]
rs900503	0.87[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs900504	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917756	chr8:60942299-61862796	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active 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	74 gene(s)	inside rSNPs	diseases
2	nsv831335	chr8:61497540-61688992	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
3	nsv890945	chr8:61522008-61707725	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv526196	chr8:61593569-61877623	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1022801	chr8:61623974-61738067	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv539632	chr8:61623974-61738067	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	esv1797364	chr8:61658362-61696231	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs876957	TOX	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:61651600-61664600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:61655000-61664800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:61655000-61665400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr8:61655600-61671400	Weak transcription	Hela-S3	cervix
5	chr8:61655800-61664400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:61655800-61666200	Weak transcription	Lung	lung
7	chr8:61656000-61664600	Weak transcription	Fetal Brain Male	brain
8	chr8:61656000-61678000	Weak transcription	Fetal Intestine Small	intestine
9	chr8:61656800-61664800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:61657000-61664400	Weak transcription	HSMM	muscle
11	chr8:61657000-61664600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr8:61657000-61690400	Weak transcription	HepG2	liver
13	chr8:61658200-61664400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr8:61658400-61683200	Weak transcription	Fetal Intestine Large	intestine
15	chr8:61661200-61664800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr8:61661200-61679000	Weak transcription	Small Intestine	intestine
17	chr8:61661400-61664600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr8:61662000-61667400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr8:61662200-61664600	Enhancers	Fetal Heart	heart
20	chr8:61662200-61666000	Enhancers	Primary T cells from cord blood	blood
21	chr8:61662400-61665800	Enhancers	Brain Hippocampus Middle	brain
22	chr8:61662600-61666200	Enhancers	Brain Substantia Nigra	brain
23	chr8:61663000-61664400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr8:61663000-61666800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr8:61663200-61664800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:61663200-61665000	Enhancers	H9 Cell Line	embryonic stem cell
27	chr8:61663200-61665000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:61663200-61665800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr8:61663400-61664400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr8:61663400-61664800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr8:61663400-61664800	Enhancers	Brain Cingulate Gyrus	brain
32	chr8:61663400-61665400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr8:61663400-61665600	Enhancers	Brain Anterior Caudate	brain
34	chr8:61663400-61665600	Enhancers	Fetal Brain Female	brain
35	chr8:61663400-61665800	Enhancers	Dnd41	blood
36	chr8:61663400-61666000	Enhancers	Fetal Lung	lung
37	chr8:61663600-61664400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr8:61663600-61664400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr8:61663600-61664400	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr8:61663600-61664600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr8:61663600-61665600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr8:61663600-61665800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr8:61663600-61666200	Enhancers	Brain Germinal Matrix	brain
44	chr8:61663800-61665000	Enhancers	Psoas Muscle	Psoas
45	chr8:61663800-61665000	Enhancers	HUVEC	blood vessel
46	chr8:61663800-61665600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr8:61663800-61665600	Enhancers	GM12878-XiMat	blood
48	chr8:61663800-61665800	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr8:61663800-61666000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr8:61663800-61666000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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