Variant report

Variant	rs10761239
Chromosome Location	chr9:96359884-96359885
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	chr11:71813631..71816103-chr9:96358029..96360517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149357	Chromatin interaction
ENSG00000238768	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10117225	0.85[CHB][hapmap]
rs10123378	0.85[CHB][hapmap]
rs10761238	0.85[CHB][hapmap]
rs10761240	0.85[CHB][hapmap]
rs10761243	0.85[CHB][hapmap]
rs10821164	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821165	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821167	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821168	0.85[CHB][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs10821181	0.85[CHB][hapmap]
rs10992791	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992792	0.85[CHB][hapmap]
rs10992797	0.85[CHB][hapmap]
rs10992804	0.90[CHB][hapmap]
rs1412048	0.85[CHB][hapmap]
rs2398845	0.85[CHB][hapmap]
rs3922729	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4568663	0.85[CHB][hapmap]
rs6479496	0.99[ASN][1000 genomes]
rs7857266	0.89[CHB][hapmap]

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	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10761239	HIATL1	cis	parietal	SCAN
rs10761239	C9orf102	cis	parietal	SCAN
rs10761239	FAM120AOS	cis	parietal	SCAN
rs10761239	GADD45G	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96341800-96362200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr9:96343400-96360600	Weak transcription	Dnd41	blood
3	chr9:96345000-96362600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr9:96347600-96360600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:96348400-96360200	Weak transcription	Primary B cells from cord blood	blood
6	chr9:96348400-96360200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:96352400-96360200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:96352400-96361000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:96352400-96384600	Weak transcription	NHLF	lung
13	chr9:96352600-96362400	Weak transcription	Fetal Lung	lung
14	chr9:96352800-96360600	Weak transcription	Thymus	Thymus
15	chr9:96352800-96360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:96353000-96360000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr9:96353000-96360400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:96353400-96360000	Weak transcription	Brain Germinal Matrix	brain
19	chr9:96354200-96361400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:96354400-96360000	Weak transcription	Fetal Brain Female	brain
21	chr9:96355000-96361800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:96355200-96360000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:96355200-96360400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:96355200-96360400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:96355200-96362600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:96355200-96362800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:96355200-96362800	Weak transcription	Brain Angular Gyrus	brain
28	chr9:96355400-96360600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr9:96355400-96361200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:96355400-96361400	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:96355600-96360000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr9:96355600-96360000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:96355600-96360600	Weak transcription	HepG2	liver
34	chr9:96356200-96360200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr9:96356200-96360600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr9:96356400-96360400	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr9:96356400-96364000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr9:96356600-96365600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:96356800-96362600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:96357000-96360000	Weak transcription	Brain Substantia Nigra	brain
41	chr9:96357000-96360200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:96357000-96360200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:96357000-96360200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:96357000-96360200	Weak transcription	Fetal Heart	heart
45	chr9:96357000-96360200	Weak transcription	Fetal Intestine Large	intestine
46	chr9:96357000-96360200	Weak transcription	Placenta	Placenta
47	chr9:96357000-96360800	Weak transcription	Adipose Nuclei	Adipose
48	chr9:96357000-96360800	Weak transcription	Colonic Mucosa	Colon
49	chr9:96357000-96361000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr9:96357000-96361000	Weak transcription	Gastric	stomach

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