Variant report

Variant	rs4910487
Chromosome Location	chr11:9687939-9687940
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	chr11:9681661..9684327-chr11:9686099..9688076,2	K562	blood:

Variant related genes	Relation type
ENSG00000239470	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10770051	0.86[EUR][1000 genomes]
rs10840283	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840284	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840285	0.87[CEU][hapmap]
rs10840286	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11042439	0.86[CEU][hapmap]
rs11042440	0.86[CEU][hapmap]
rs11042441	0.86[CEU][hapmap]
rs11042457	1.00[ASN][1000 genomes]
rs11042462	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042464	1.00[ASN][1000 genomes]
rs11042466	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042467	1.00[ASN][1000 genomes]
rs11042486	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11042500	1.00[CHB][hapmap]
rs11042511	1.00[CHB][hapmap]
rs11600183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11601008	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603527	1.00[ASN][1000 genomes]
rs11607321	1.00[ASN][1000 genomes]
rs11607776	0.81[EUR][1000 genomes]
rs11607900	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362879	1.00[ASN][1000 genomes]
rs12364089	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421878	1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12786236	1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs12789209	1.00[ASN][1000 genomes]
rs12789429	1.00[ASN][1000 genomes]
rs12794270	1.00[ASN][1000 genomes]
rs12797744	1.00[ASN][1000 genomes]
rs12801958	1.00[ASN][1000 genomes]
rs12803440	1.00[ASN][1000 genomes]
rs12805683	1.00[ASN][1000 genomes]
rs12807017	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808226	1.00[CHB][hapmap]
rs17268632	1.00[CHB][hapmap]
rs34063054	1.00[ASN][1000 genomes]
rs35806232	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089180	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910060	1.00[ASN][1000 genomes]
rs4910486	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910488	1.00[ASN][1000 genomes]
rs4910492	1.00[ASN][1000 genomes]
rs4910493	1.00[ASN][1000 genomes]
rs4910497	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4910505	1.00[CHB][hapmap]
rs56043731	1.00[ASN][1000 genomes]
rs67867011	1.00[ASN][1000 genomes]
rs7120616	0.86[CEU][hapmap]
rs72852112	1.00[ASN][1000 genomes]
rs7943610	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4910487	TRIM22	cis	cerebellum	SCAN
rs4910487	OR2D2	cis	cerebellum	SCAN
rs4910487	LCORL	trans	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9685200-9688800	Active TSS	GM12878-XiMat	blood
2	chr11:9685400-9688200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr11:9686600-9688800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:9686600-9688800	Weak transcription	Spleen	Spleen
5	chr11:9686600-9696000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:9686600-9702000	Weak transcription	Left Ventricle	heart
7	chr11:9686600-9702600	Weak transcription	Gastric	stomach
8	chr11:9686600-9704600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:9686600-9709600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:9686600-9711200	Weak transcription	Esophagus	oesophagus
11	chr11:9686800-9688000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:9686800-9696600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:9686800-9696800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:9686800-9710800	Weak transcription	Aorta	Aorta
15	chr11:9686800-9716400	Weak transcription	Ovary	ovary
16	chr11:9687000-9688000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:9687000-9688000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
18	chr11:9687000-9688000	ZNF genes & repeats	Brain Anterior Caudate	brain
19	chr11:9687000-9688000	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr11:9687000-9688000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
21	chr11:9687000-9688200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:9687000-9688200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:9687000-9688200	ZNF genes & repeats	A549	lung
24	chr11:9687000-9688600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:9687000-9689400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
26	chr11:9687000-9697200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr11:9687200-9688000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:9687200-9688000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:9687200-9688000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:9687200-9688000	ZNF genes & repeats	Psoas Muscle	Psoas
31	chr11:9687200-9688400	ZNF genes & repeats	NHDF-Ad	bronchial
32	chr11:9687200-9688600	Weak transcription	Placenta	Placenta
33	chr11:9687200-9688800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr11:9687200-9694200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr11:9687200-9694400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:9687200-9694400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:9687200-9694400	Weak transcription	Osteobl	bone
38	chr11:9687200-9696600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:9687200-9696600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:9687200-9697200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:9687200-9702600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr11:9687200-9705000	Weak transcription	HSMM	muscle
43	chr11:9687200-9709400	Weak transcription	HSMMtube	muscle
44	chr11:9687200-9710200	Weak transcription	Hela-S3	cervix
45	chr11:9687400-9688000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr11:9687400-9688200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:9687400-9688200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:9687400-9689400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
49	chr11:9687400-9691600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr11:9687400-9694200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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