Variant report

Variant	rs2001945
Chromosome Location	chr8:126477978-126477979
allele	C/G
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	TEAD4	chr8:126477848-126478344	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr8:126477653-126478496	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr8:126477659-126479594	ECC-1	luminal epithelium:	n/a	chr8:126479568-126479577
4	ZNF143	chr8:126477971-126478171	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr8:126477964-126478342	HCT-116	colon:	n/a	n/a
6	TCF12	chr8:126477683-126479561	ECC-1	luminal epithelium:	n/a	chr8:126478959-126478967 chr8:126479277-126479286
7	NFIC	chr8:126477500-126478461	ECC-1	luminal epithelium:	n/a	n/a
8	TAF1	chr8:126477956-126478331	PFSK-1	brain:	n/a	n/a
9	TEAD4	chr8:126477783-126478486	ECC-1	luminal epithelium:	n/a	n/a
10	TCF12	chr8:126477753-126478523	ECC-1	luminal epithelium:	n/a	n/a
11	RAD21	chr8:126477829-126478429	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:126476379..126479143-chr8:126667265..126669380,2	MCF-7	breast:
2	chr8:126442745..126445381-chr8:126476232..126477978,2	MCF-7	breast:
3	chr8:126465262..126466889-chr8:126476635..126478328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253111	TF binding region
ENSG00000173334	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17321515	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs2001844	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2001846	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2954017	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2954019	0.85[CEU][hapmap]
rs2954021	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2954022	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2954029	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2954031	0.83[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2980853	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.94[ASN][1000 genomes]
rs2980854	0.85[CEU][hapmap]
rs2980855	0.85[CEU][hapmap]
rs2980856	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs2980860	0.92[ASN][1000 genomes]
rs2980868	0.89[ASN][1000 genomes]
rs2980869	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[ASN][1000 genomes]
rs2980871	0.82[CEU][hapmap]
rs2980875	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.92[ASN][1000 genomes]
rs2980882	0.94[ASN][1000 genomes]
rs2980886	0.92[ASN][1000 genomes]
rs6982502	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6982636	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891437	chr8:126470817-126629328	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Triglycerides	21909109	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2001945	C8orf76	cis	cerebellum	SCAN
rs2001945	HAS2	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:126464800-126478000	Weak transcription	Gastric	stomach
2	chr8:126472400-126479000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:126475400-126479200	Weak transcription	A549	lung
4	chr8:126475600-126478000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr8:126475600-126478200	Weak transcription	HepG2	liver
6	chr8:126475600-126478800	Weak transcription	K562	blood
7	chr8:126475800-126479600	Enhancers	Placenta	Placenta
8	chr8:126476400-126478800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr8:126476400-126479000	Weak transcription	Right Ventricle	heart
10	chr8:126476600-126478000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr8:126476600-126478800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:126476600-126478800	Enhancers	Hela-S3	cervix
13	chr8:126476600-126479000	Weak transcription	Liver	Liver
14	chr8:126476600-126483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:126476800-126479000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:126476800-126479200	Weak transcription	NHEK	skin
17	chr8:126477000-126479800	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr8:126477200-126479800	Enhancers	HUVEC	blood vessel
19	chr8:126477400-126479400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr8:126477400-126479600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:126477400-126485000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr8:126477600-126478800	Enhancers	Fetal Kidney	kidney
23	chr8:126477600-126479400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr8:126477600-126479400	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr8:126477600-126479400	Enhancers	Adipose Nuclei	Adipose
26	chr8:126477600-126479400	Enhancers	Fetal Stomach	stomach
27	chr8:126477600-126479400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr8:126477600-126479400	Enhancers	Spleen	Spleen
29	chr8:126477600-126479600	Enhancers	Fetal Muscle Leg	muscle
30	chr8:126477600-126479600	Enhancers	NH-A	brain
31	chr8:126477600-126479800	Enhancers	Fetal Lung	lung
32	chr8:126477600-126480000	Enhancers	Fetal Muscle Trunk	muscle
33	chr8:126477800-126478000	Enhancers	Primary hematopoietic stem cells	blood
34	chr8:126477800-126478000	Enhancers	Colon Smooth Muscle	Colon
35	chr8:126477800-126478000	Enhancers	Fetal Brain Female	brain
36	chr8:126477800-126478200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr8:126477800-126478200	Enhancers	Primary B cells from cord blood	blood
38	chr8:126477800-126479200	Enhancers	Brain Hippocampus Middle	brain
39	chr8:126477800-126479400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr8:126477800-126479400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:126477800-126479400	Enhancers	Left Ventricle	heart
42	chr8:126477800-126479400	Enhancers	Lung	lung
43	chr8:126477800-126479400	Enhancers	Ovary	ovary
44	chr8:126477800-126479400	Enhancers	Right Atrium	heart
45	chr8:126477800-126479600	Enhancers	Fetal Heart	heart
46	chr8:126477800-126479600	Enhancers	HSMM	muscle
47	chr8:126477800-126479800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr8:126477800-126479800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr8:126477800-126480000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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