Variant report

Variant	rs1939799
Chromosome Location	chr11:105966591-105966592
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	chr11:105965185..105968014-chr11:105969595..105971364,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10791780	0.90[CHB][hapmap]
rs10895899	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10895900	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap]
rs10895904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11226915	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11226920	0.85[CHB][hapmap]
rs11226922	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11226931	0.85[ASN][1000 genomes]
rs12365489	0.90[CHB][hapmap]
rs17105049	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs1893174	0.90[CHB][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs1939798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1940772	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2155340	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2186731	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277278	0.81[ASN][1000 genomes]
rs3740869	0.80[CHB][hapmap]
rs4237618	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4440991	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4474407	0.90[CHB][hapmap]
rs4485076	0.81[EUR][1000 genomes]
rs4565867	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4754141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60606604	0.81[ASN][1000 genomes]
rs7108636	0.85[CHB][hapmap]
rs7130759	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7131047	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754562	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs7554	0.90[CHB][hapmap]
rs766717	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs9651674	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs9943677	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1048381	chr11:105945117-106561574	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1939799	AASDHPPT	cis	lymphoblastoid	seeQTL
rs1939799	KDELC2	cis	cerebellum	SCAN
rs1939799	AASDHPPT	Cis_1M	lymphoblastoid	RTeQTL
rs1939799	MMP12	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105949000-105973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:105949200-105967800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:105949200-105969800	Weak transcription	Lung	lung
4	chr11:105949200-105971600	Weak transcription	Esophagus	oesophagus
5	chr11:105950400-105971200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:105950600-105969400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr11:105952000-105969400	Weak transcription	Colonic Mucosa	Colon
8	chr11:105953400-105970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:105953600-105969600	Weak transcription	Gastric	stomach
10	chr11:105956000-105970000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr11:105957200-105971000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:105957200-105976600	Weak transcription	Pancreas	Pancrea
13	chr11:105957200-105976800	Weak transcription	Aorta	Aorta
14	chr11:105957800-105968200	Weak transcription	Psoas Muscle	Psoas
15	chr11:105958600-105970000	Weak transcription	Fetal Intestine Small	intestine
16	chr11:105958600-105971800	Weak transcription	Hela-S3	cervix
17	chr11:105959000-105969000	Weak transcription	Stomach Mucosa	stomach
18	chr11:105959200-105970000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:105959200-105970400	Strong transcription	Dnd41	blood
20	chr11:105959400-105970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr11:105959400-105970200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr11:105959600-105967200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:105959800-105970200	Weak transcription	Small Intestine	intestine
24	chr11:105959800-105970400	Weak transcription	Fetal Brain Male	brain
25	chr11:105960200-105967800	Weak transcription	Fetal Heart	heart
26	chr11:105961000-105968600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:105961000-105969000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr11:105961000-105969400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:105961000-105969600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:105961000-105970800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:105961000-105970800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:105961200-105967000	Strong transcription	K562	blood
33	chr11:105961200-105969200	Strong transcription	Fetal Thymus	thymus
34	chr11:105961200-105970200	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:105961200-105970400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:105961400-105968400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:105961400-105968400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:105961400-105968800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr11:105961400-105968800	Strong transcription	Primary T cells from cord blood	blood
40	chr11:105961400-105969000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:105961400-105969200	Strong transcription	Fetal Lung	lung
42	chr11:105961400-105970400	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr11:105961400-105970400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:105961400-105971600	Strong transcription	HSMM	muscle
45	chr11:105961600-105966800	Strong transcription	Brain Germinal Matrix	brain
46	chr11:105961600-105968600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:105961600-105968800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr11:105961600-105968800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr11:105961600-105970400	Strong transcription	Adipose Nuclei	Adipose
50	chr11:105961600-105970400	Strong transcription	Liver	Liver

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