Variant report

Variant	rs10992049
Chromosome Location	chr9:92855977-92855978
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	chr9:92219469..92221520-chr9:92854815..92856417,2	MCF-7	breast:
2	chr9:92219124..92221595-chr9:92854778..92859945,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130222	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10122998	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790815	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11792422	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346907	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12552603	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553616	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553823	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1329046	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16906191	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718362	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs423239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048555	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651746	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73651747	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv893563	chr9:92816727-92967125	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10992049	GOLM1	cis	parietal	SCAN
rs10992049	AUH	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92848400-92858000	Weak transcription	Right Atrium	heart
2	chr9:92848800-92857800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:92848800-92862200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:92849000-92856000	Weak transcription	Fetal Brain Female	brain
5	chr9:92854200-92856200	Enhancers	Fetal Thymus	thymus
6	chr9:92854400-92856200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr9:92854400-92856400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr9:92854600-92856000	Enhancers	Dnd41	blood
9	chr9:92854600-92856200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr9:92854600-92856400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr9:92854800-92856000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr9:92854800-92856400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr9:92854800-92856400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr9:92855000-92856000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:92855000-92856000	Enhancers	Fetal Muscle Trunk	muscle
16	chr9:92855000-92856200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:92855000-92856400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr9:92855000-92858000	Enhancers	Fetal Muscle Leg	muscle
19	chr9:92855200-92856000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:92855400-92856200	Enhancers	GM12878-XiMat	blood
21	chr9:92855400-92857800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr9:92855400-92857800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:92855600-92856000	Weak transcription	HSMMtube	muscle
24	chr9:92855600-92856400	Enhancers	Primary T cells from cord blood	blood
25	chr9:92855600-92857800	Weak transcription	Pancreas	Pancrea
26	chr9:92855600-92864400	Weak transcription	Brain Cingulate Gyrus	brain

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