Variant report

Variant	rs10840129
Chromosome Location	chr11:8829494-8829495
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8708349..8711473-chr11:8829326..8831114,3	K562	blood:
2	chr11:8706888..8711251-chr11:8829326..8831400,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM66-7	chr11:8829373-8832882	NONHSAT017885

Variant related genes	Relation type
ENSG00000212607	Chromatin interaction
ENSG00000166441	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10522860	0.95[ASN][1000 genomes]
rs10734638	0.94[CEU][hapmap]
rs10840127	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042070	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11042072	1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11042099	0.94[CEU][hapmap]
rs1133833	0.94[CEU][hapmap]
rs16906056	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337866	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2568029	0.94[CEU][hapmap];0.85[MEX][hapmap]
rs2568035	0.92[CEU][hapmap]
rs2568056	0.94[CEU][hapmap]
rs2653558	0.94[CEU][hapmap]
rs2653591	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2742502	0.94[CEU][hapmap]
rs34023999	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34033747	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34275210	0.83[EUR][1000 genomes]
rs34417491	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34418236	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35503692	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35563381	0.84[EUR][1000 genomes]
rs35909878	0.83[EUR][1000 genomes]
rs36094920	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36180552	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3850934	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3915868	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910068	0.94[CEU][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs4929915	0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7117900	0.94[CEU][hapmap]
rs7127197	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7936201	0.81[MEX][hapmap]
rs7950491	0.92[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised 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 target site	34 gene(s)	inside rSNPs	diseases
3	nsv527920	chr11:8816695-8856822	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv527073	chr11:8829168-8848463	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10840129	AMPD3	cis	parietal	SCAN
rs10840129	C11orf17	cis	cerebellum	SCAN
rs10840129	C11orf17	cis	lymphoblastoid	seeQTL
rs10840129	OR52A1	cis	parietal	SCAN
rs10840129	RPL27A	cis	cerebellum	SCAN
rs10840129	PRKCDBP	cis	parietal	SCAN
rs10840129	TMEM9B	cis	parietal	SCAN
rs10840129	RPL27A	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8809000-8830200	Weak transcription	Fetal Brain Male	brain
2	chr11:8811800-8830400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:8811800-8830600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:8816400-8831800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:8816600-8830000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:8816600-8830600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:8819800-8829800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:8821600-8830200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr11:8824200-8830400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:8825400-8830400	Enhancers	Left Ventricle	heart
11	chr11:8825600-8829600	Enhancers	Gastric	stomach
12	chr11:8826400-8829800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:8826400-8830600	Enhancers	Brain Angular Gyrus	brain
14	chr11:8826600-8830200	Enhancers	Pancreas	Pancrea
15	chr11:8827400-8830400	Enhancers	Psoas Muscle	Psoas
16	chr11:8827400-8831200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:8827600-8830600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:8827600-8831000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr11:8827800-8829800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:8827800-8830200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:8827800-8830800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:8828000-8830000	Enhancers	Esophagus	oesophagus
23	chr11:8828000-8830800	Enhancers	Brain Germinal Matrix	brain
24	chr11:8828200-8829600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:8828200-8829600	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr11:8828200-8830200	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr11:8828200-8830200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr11:8828200-8830400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr11:8828200-8831000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr11:8828400-8829800	Flanking Active TSS	Colonic Mucosa	Colon
31	chr11:8828400-8830000	Enhancers	Lung	lung
32	chr11:8828400-8830400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:8828400-8831000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:8828600-8829600	Flanking Active TSS	Fetal Muscle Trunk	muscle
35	chr11:8828600-8830000	Enhancers	Fetal Intestine Large	intestine
36	chr11:8828600-8830000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr11:8828600-8830600	Enhancers	Fetal Intestine Small	intestine
38	chr11:8828600-8830800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
39	chr11:8828600-8830800	Flanking Active TSS	Stomach Mucosa	stomach
40	chr11:8828600-8830800	Flanking Active TSS	HMEC	breast
41	chr11:8828600-8831000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr11:8828600-8831200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:8828600-8831200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:8828600-8831200	Flanking Active TSS	HSMMtube	muscle
45	chr11:8828600-8831200	Flanking Active TSS	NHEK	skin
46	chr11:8828600-8831400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr11:8828600-8831400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr11:8828800-8829600	Enhancers	H1 Cell Line	embryonic stem cell
49	chr11:8828800-8830200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:8828800-8830200	Enhancers	Spleen	Spleen

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