Variant report

Variant	rs41491746
Chromosome Location	chr18:11999326-11999327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr18:11999300-11999450	AG10803	skin:	n/a	n/a
2	CTCF	chr18:11999320-11999470	HFF-Myc	foreskin:	n/a	n/a
3	CTCF	chr18:11999320-11999470	NHDF-neo	bronchial:	n/a	n/a
4	CTCF	chr18:11999320-11999550	A549	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000266955	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1122199	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16976875	0.85[JPT][hapmap]
rs16976886	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2360082	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3786305	0.82[CHD][hapmap];0.80[ASN][1000 genomes]
rs4455029	0.81[JPT][hapmap]
rs45442994	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55638894	0.96[ASN][1000 genomes]
rs60232438	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs971363	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982400-12005000	Weak transcription	Aorta	Aorta
2	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
3	chr18:11993400-11999400	Enhancers	Fetal Muscle Leg	muscle
4	chr18:11993400-12016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr18:11995400-12001800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr18:11995600-11999400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr18:11995600-12014400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:11995800-11999400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr18:11996000-12001400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr18:11996000-12001400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:11996000-12004000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr18:11996000-12004800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr18:11996000-12004800	Weak transcription	HMEC	breast
14	chr18:11996000-12005600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr18:11996200-11999400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr18:11996200-11999600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr18:11996200-12004800	Weak transcription	NHEK	skin
18	chr18:11996200-12005200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:11996200-12005600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr18:11996200-12012200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr18:11996200-12014800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr18:11996200-12015400	Weak transcription	Brain Anterior Caudate	brain
23	chr18:11996400-12001400	Weak transcription	Thymus	Thymus
24	chr18:11996400-12002200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr18:11996400-12004000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr18:11996400-12005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:11996400-12007800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr18:11996600-12005000	Weak transcription	GM12878-XiMat	blood
29	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
30	chr18:11996800-11999600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr18:11996800-12001000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr18:11996800-12001400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr18:11996800-12017200	Weak transcription	Fetal Thymus	thymus
34	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
35	chr18:11997000-12004800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr18:11997600-11999400	Weak transcription	Colonic Mucosa	Colon
38	chr18:11998000-11999800	Enhancers	HSMMtube	muscle
39	chr18:11998000-12001400	Enhancers	Liver	Liver
40	chr18:11998400-12000000	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr18:11998400-12001200	Weak transcription	Fetal Lung	lung
42	chr18:11998400-12006000	Weak transcription	Brain Angular Gyrus	brain
43	chr18:11998400-12013200	Weak transcription	Right Atrium	heart
44	chr18:11998400-12014400	Weak transcription	Psoas Muscle	Psoas
45	chr18:11998400-12015200	Weak transcription	Brain Hippocampus Middle	brain
46	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr18:11998600-11999400	Weak transcription	Gastric	stomach
48	chr18:11998600-11999600	Weak transcription	Adipose Nuclei	Adipose
49	chr18:11998600-12002600	Enhancers	Stomach Mucosa	stomach
50	chr18:11998600-12005000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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