Variant report

Variant	rs11006119
Chromosome Location	chr10:52315912-52315913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:52313061..52318898-chr10:52381919..52385253,10	MCF-7	breast:
2	chr10:52315809..52317364-chr10:52382275..52385092,2	K562	blood:
3	chr10:52313474..52316249-chr10:52319945..52321727,3	K562	blood:
4	chr10:52315239..52317200-chr10:52324724..52326608,3	K562	blood:
5	chr10:52313546..52319488-chr10:52380502..52386285,13	K562	blood:
6	chr10:52313555..52316104-chr10:52337795..52339466,2	K562	blood:
7	chr10:52310270..52314455-chr10:52315610..52319835,4	MCF-7	breast:
8	chr10:52315813..52318278-chr10:52376288..52379260,2	K562	blood:
9	chr10:52314491..52316495-chr10:52365802..52367749,2	MCF-7	breast:
10	chr10:52310656..52316983-chr10:52334408..52339466,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000230036	Chromatin interaction
ENSG00000226200	Chromatin interaction
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10763584	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs10763585	0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10826234	0.94[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs11006102	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006155	0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11006436	0.82[YRI][hapmap]
rs11006438	0.82[YRI][hapmap]
rs12358162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2208036	0.83[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2860472	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2983360	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2983364	0.94[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3011707	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3011710	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs3011802	0.91[ASN][1000 genomes]
rs3920545	0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap]
rs4475874	0.82[YRI][hapmap]
rs4935731	1.00[ASN][1000 genomes]
rs4935732	1.00[ASN][1000 genomes]
rs55669848	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55735989	0.89[ASN][1000 genomes]
rs56403030	1.00[ASN][1000 genomes]
rs61858108	1.00[ASN][1000 genomes]
rs6481433	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7074405	0.87[ASN][1000 genomes]
rs7075104	0.89[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs7088807	0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs7898315	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers 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	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11006119	LRRC18	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52280200-52328000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:52299600-52320600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:52300800-52322800	Weak transcription	Primary B cells from cord blood	blood
4	chr10:52301600-52327200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:52305400-52329600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr10:52306000-52316000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:52306000-52319000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:52306000-52321400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:52306000-52322000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:52306000-52331800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr10:52308000-52337200	Weak transcription	Primary T cells from cord blood	blood
12	chr10:52309600-52316400	Enhancers	Brain Substantia Nigra	brain
13	chr10:52310400-52316000	Weak transcription	Lung	lung
14	chr10:52310400-52323800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr10:52310600-52316000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr10:52310600-52323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr10:52310600-52327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr10:52311000-52323600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:52311000-52335800	Weak transcription	Esophagus	oesophagus
20	chr10:52311600-52316800	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr10:52312000-52316600	Enhancers	Brain Angular Gyrus	brain
22	chr10:52312000-52317000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr10:52312600-52321000	Weak transcription	NH-A	brain
24	chr10:52312800-52316000	Enhancers	Brain Cingulate Gyrus	brain
25	chr10:52312800-52319800	Enhancers	NHLF	lung
26	chr10:52312800-52335800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr10:52312800-52335800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr10:52313000-52316200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr10:52313000-52316600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr10:52313000-52316800	Enhancers	Brain Hippocampus Middle	brain
31	chr10:52313000-52317000	Enhancers	Brain Anterior Caudate	brain
32	chr10:52313000-52317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:52313000-52319200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr10:52313000-52320600	Weak transcription	HepG2	liver
35	chr10:52313000-52322800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr10:52313200-52333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:52313600-52316400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:52313600-52316800	Enhancers	Left Ventricle	heart
39	chr10:52313600-52317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr10:52313600-52337400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr10:52313800-52316800	Enhancers	Colon Smooth Muscle	Colon
42	chr10:52313800-52316800	Enhancers	Pancreas	Pancrea
43	chr10:52313800-52320800	Weak transcription	Fetal Kidney	kidney
44	chr10:52314000-52316800	Enhancers	Right Atrium	heart
45	chr10:52314000-52316800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr10:52314200-52316000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr10:52314200-52316200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr10:52314200-52316200	Enhancers	Fetal Stomach	stomach
49	chr10:52314200-52316400	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr10:52314200-52316400	Enhancers	Fetal Muscle Leg	muscle

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