Variant report

Variant	rs11140009
Chromosome Location	chr9:85910642-85910643
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	chr9:85910411..85912906-chr9:85925285..85927422,2	MCF-7	breast:
2	chr9:85908596..85911105-chr9:85914154..85916205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172159	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10512138	0.81[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs10867979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11139998	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11140001	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11140010	0.83[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12339855	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12376739	0.81[CHB][hapmap];0.85[CHD][hapmap];0.80[JPT][hapmap]
rs1323778	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs1323779	0.94[ASN][1000 genomes]
rs1323782	1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs1323785	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17086124	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4395967	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs55707933	0.85[ASN][1000 genomes]
rs6559718	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034332	0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap]
rs7856762	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv6586	chr9:85869828-85914812	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11140009	NTRK2	cis	parietal	SCAN
rs11140009	RASEF	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85866200-85913000	Weak transcription	Aorta	Aorta
2	chr9:85884200-85912400	Weak transcription	HepG2	liver
3	chr9:85895000-85912800	Weak transcription	Fetal Brain Female	brain
4	chr9:85896000-85913600	Weak transcription	Psoas Muscle	Psoas
5	chr9:85896000-85919800	Weak transcription	Lung	lung
6	chr9:85896400-85912600	Weak transcription	Gastric	stomach
7	chr9:85896400-85913400	Weak transcription	Brain Germinal Matrix	brain
8	chr9:85896600-85913000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr9:85896800-85910800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr9:85896800-85922800	Weak transcription	Spleen	Spleen
11	chr9:85897000-85912600	Weak transcription	Adipose Nuclei	Adipose
12	chr9:85897000-85912600	Weak transcription	Ovary	ovary
13	chr9:85897000-85912800	Weak transcription	Right Ventricle	heart
14	chr9:85897200-85912000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr9:85897200-85913000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:85897200-85919200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:85897200-85922000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr9:85897400-85914800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr9:85905800-85919000	Weak transcription	Fetal Stomach	stomach
20	chr9:85906000-85911600	Weak transcription	Left Ventricle	heart
21	chr9:85906400-85915000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:85906600-85919400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:85906800-85919600	Weak transcription	Pancreas	Pancrea
24	chr9:85908400-85913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:85908400-85913800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr9:85908800-85913000	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:85909000-85914200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:85909000-85918400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:85909200-85928000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:85910000-85913600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:85910400-85918000	Weak transcription	Fetal Brain Male	brain
32	chr9:85910600-85911600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr9:85910600-85914000	Strong transcription	Monocytes-CD14+_RO01746	blood

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