Variant report

Variant	rs11669516
Chromosome Location	chr19:19532682-19532683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19532624..19534313-chr19:19536405..19538480,2	MCF-7	breast:
2	chr19:19532571..19534201-chr19:19541059..19542925,2	K562	blood:

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1000237	0.93[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10282	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs10401193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10402308	0.92[CHB][hapmap]
rs10402451	0.87[ASN][1000 genomes]
rs10402627	0.85[ASN][1000 genomes]
rs10404728	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10405625	0.91[ASN][1000 genomes]
rs10410664	0.91[ASN][1000 genomes]
rs10414830	0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10419912	0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10422819	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1047361	0.87[ASN][1000 genomes]
rs1054284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1054930	0.81[ASN][1000 genomes]
rs1063966	0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs12972397	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12973258	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12975119	0.91[ASN][1000 genomes]
rs12977524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981405	0.82[ASN][1000 genomes]
rs12983940	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1465695	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469712	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1469713	0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs16996148	0.91[YRI][hapmap]
rs17288409	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1808653	0.87[ASN][1000 genomes]
rs1858999	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs1859287	0.80[JPT][hapmap]
rs1865034	0.87[ASN][1000 genomes]
rs2023883	0.80[JPT][hapmap]
rs2082421	0.95[ASN][1000 genomes]
rs2099333	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2099334	0.91[ASN][1000 genomes]
rs2163804	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2163805	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288852	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2304098	0.92[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2315279	0.81[ASN][1000 genomes]
rs2315610	0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs28478453	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905431	0.81[ASN][1000 genomes]
rs2916069	0.84[ASN][1000 genomes]
rs2916073	0.91[ASN][1000 genomes]
rs2916074	0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2916076	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2965180	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs2965182	0.91[ASN][1000 genomes]
rs2965183	0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2965188	0.93[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2965189	0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs34277109	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs34647936	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35418933	0.80[ASN][1000 genomes]
rs3752151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3764567	0.80[JPT][hapmap]
rs3794990	0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3794993	0.92[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4808196	0.84[EUR][1000 genomes]
rs4808198	0.90[ASN][1000 genomes]
rs4808199	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808200	0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808202	0.91[ASN][1000 genomes]
rs4808203	0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808208	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs4808950	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808955	0.90[ASN][1000 genomes]
rs4808957	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808959	0.93[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808960	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808961	0.93[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4808964	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4808965	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808967	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs60003758	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60321073	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6511036	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511038	0.85[ASN][1000 genomes]
rs6909	0.92[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs7245983	0.93[CHB][hapmap];0.82[JPT][hapmap]
rs7250658	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7250893	0.84[ASN][1000 genomes]
rs7252888	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7253807	0.82[ASN][1000 genomes]
rs7256149	0.93[ASN][1000 genomes]
rs7258508	0.81[EUR][1000 genomes]
rs7259434	0.81[JPT][hapmap]
rs747050	0.93[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs751856	0.87[ASN][1000 genomes]
rs751858	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs754255	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs892021	0.93[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs892022	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9917108	0.90[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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11669516	KIAA0892	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19518600-19549800	Weak transcription	Fetal Brain Female	brain
2	chr19:19520800-19546800	Weak transcription	Hela-S3	cervix
3	chr19:19521000-19545400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:19521800-19536200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:19521800-19537600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:19522000-19545000	Weak transcription	Fetal Lung	lung
7	chr19:19522200-19534600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:19522200-19548600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr19:19522200-19563400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:19522600-19533200	Weak transcription	Aorta	Aorta
11	chr19:19522600-19533600	Weak transcription	Fetal Stomach	stomach
12	chr19:19522600-19537600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:19525400-19538200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr19:19526400-19535000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:19526600-19533400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr19:19526600-19533600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr19:19527000-19533200	Enhancers	Primary B cells from peripheral blood	blood
18	chr19:19527000-19534400	Enhancers	Fetal Muscle Trunk	muscle
19	chr19:19527000-19535600	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:19527600-19533200	Enhancers	Fetal Muscle Leg	muscle
21	chr19:19528000-19533400	Enhancers	Spleen	Spleen
22	chr19:19528600-19532800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:19528800-19539000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:19528800-19544200	Weak transcription	Fetal Heart	heart
25	chr19:19529000-19537000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:19529000-19539000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:19529200-19537400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:19530000-19539000	Weak transcription	Placenta	Placenta
29	chr19:19530000-19539000	Weak transcription	NHLF	lung
30	chr19:19530000-19545400	Weak transcription	Colonic Mucosa	Colon
31	chr19:19530200-19533800	Weak transcription	Osteobl	bone
32	chr19:19530200-19537000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:19530200-19537800	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:19530200-19543400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr19:19530200-19547400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr19:19530400-19536800	Strong transcription	Fetal Intestine Small	intestine
37	chr19:19531200-19532800	Enhancers	Right Ventricle	heart
38	chr19:19531200-19533200	Enhancers	Left Ventricle	heart
39	chr19:19531200-19533400	Enhancers	Esophagus	oesophagus
40	chr19:19531200-19538000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:19531400-19533200	Enhancers	Gastric	stomach
42	chr19:19531400-19534800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr19:19531400-19541600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:19531400-19545000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr19:19531600-19533200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:19531600-19534800	Enhancers	Pancreas	Pancrea
47	chr19:19531600-19535600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:19531600-19535600	Enhancers	Lung	lung
49	chr19:19531600-19537400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr19:19531800-19533200	Enhancers	Psoas Muscle	Psoas

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