Variant report

Variant	rs16911662
Chromosome Location	chr9:116779918-116779919
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	chr9:116778931..116781819-chr9:116782880..116785170,2	MCF-7	breast:
2	chr9:116773678..116775995-chr9:116779298..116781749,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10114580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10982039	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12349112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1576467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16912115	1.00[MEX][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55823556	1.00[EUR][1000 genomes]
rs57447464	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57659453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58238706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58769230	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59445762	1.00[EUR][1000 genomes]
rs60351204	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs60401186	1.00[EUR][1000 genomes]
rs60562588	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61047963	1.00[EUR][1000 genomes]
rs73658311	1.00[EUR][1000 genomes]
rs73658312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73658313	1.00[EUR][1000 genomes]
rs73658314	1.00[EUR][1000 genomes]
rs73658316	1.00[EUR][1000 genomes]
rs73658317	1.00[EUR][1000 genomes]
rs73658320	1.00[EUR][1000 genomes]
rs73658321	1.00[EUR][1000 genomes]
rs7846976	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7849443	1.00[ASN][1000 genomes]
rs7863003	0.88[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	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers 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 miRNA target site	165 gene(s)	inside rSNPs	diseases
2	nsv521361	chr9:116774010-116780992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16911662	CHI3L2	trans	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116733400-116800200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116736400-116783000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:116756800-116783800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:116757000-116783400	Weak transcription	Small Intestine	intestine
5	chr9:116762200-116780400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr9:116764600-116797200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:116765000-116783200	Weak transcription	NHEK	skin
8	chr9:116765800-116784400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:116766000-116784800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:116766000-116792600	Weak transcription	Stomach Mucosa	stomach
11	chr9:116766000-116798000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:116766200-116799000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:116766600-116782400	Strong transcription	A549	lung
14	chr9:116766600-116811200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:116767000-116780400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:116767200-116785800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:116768400-116794600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:116768800-116784800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:116769400-116780200	Weak transcription	Thymus	Thymus
20	chr9:116769400-116790400	Weak transcription	Right Ventricle	heart
21	chr9:116773600-116809200	Weak transcription	Fetal Heart	heart
22	chr9:116774000-116780400	Weak transcription	Brain Substantia Nigra	brain
23	chr9:116774000-116791200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr9:116774000-116791200	Weak transcription	Fetal Brain Male	brain
25	chr9:116774200-116783800	Weak transcription	HMEC	breast
26	chr9:116774200-116798400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr9:116774600-116790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:116775200-116783400	Weak transcription	NH-A	brain
29	chr9:116775400-116780400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:116775400-116784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:116775600-116783000	Strong transcription	Fetal Lung	lung
32	chr9:116776200-116789800	Strong transcription	HUVEC	blood vessel
33	chr9:116776400-116782400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:116776600-116780000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:116776800-116781600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:116777000-116782000	Weak transcription	HSMM	muscle
37	chr9:116777400-116781200	Strong transcription	Osteobl	bone
38	chr9:116777800-116782200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:116777800-116785000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:116778000-116781200	Strong transcription	Fetal Muscle Leg	muscle
41	chr9:116778000-116781400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:116778000-116781800	Strong transcription	Fetal Stomach	stomach
43	chr9:116778000-116785200	Strong transcription	NHDF-Ad	bronchial
44	chr9:116778200-116781400	Strong transcription	Fetal Intestine Small	intestine
45	chr9:116778200-116781800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:116778400-116780600	Strong transcription	Ovary	ovary
47	chr9:116778400-116781000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr9:116778400-116781600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr9:116778400-116781600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:116778400-116781800	Strong transcription	Fetal Muscle Trunk	muscle

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