Variant report

Variant	rs11874712
Chromosome Location	chr18:43688576-43688577
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:43683649..43685895-chr18:43688499..43690825,2	K562	blood:
2	chr18:43673300..43675362-chr18:43687086..43690045,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152234	Chromatin interaction
ENSG00000152240	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11082509	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11082510	0.87[EUR][1000 genomes]
rs11659357	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11659795	0.93[EUR][1000 genomes]
rs11661945	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11664314	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11664534	0.88[ASN][1000 genomes]
rs11664743	1.00[JPT][hapmap]
rs11664764	0.93[EUR][1000 genomes]
rs11872954	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872985	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12954405	0.88[ASN][1000 genomes]
rs12954944	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12955201	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12959752	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12959909	0.88[ASN][1000 genomes]
rs13381709	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1800636	1.00[CEU][hapmap]
rs1800637	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1800639	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1800640	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2298787	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs28457840	0.85[EUR][1000 genomes]
rs28504655	0.92[EUR][1000 genomes]
rs28532950	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28699609	0.94[EUR][1000 genomes]
rs28757346	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34907121	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35507656	0.86[EUR][1000 genomes]
rs36111316	0.88[ASN][1000 genomes]
rs3765636	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs56075249	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56181324	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62096500	0.93[EUR][1000 genomes]
rs71364522	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs718515	1.00[JPT][hapmap]
rs7230064	0.89[EUR][1000 genomes]
rs7235373	0.86[EUR][1000 genomes]
rs7240076	1.00[JPT][hapmap]
rs7244921	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7244950	0.94[EUR][1000 genomes]
rs7359798	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7359800	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8083998	0.94[EUR][1000 genomes]
rs8085444	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8088881	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs8089150	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8089153	1.00[JPT][hapmap]
rs8091452	0.82[EUR][1000 genomes]
rs8092674	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs8093880	0.93[EUR][1000 genomes]
rs8094902	0.93[EUR][1000 genomes]
rs8095031	0.93[EUR][1000 genomes]
rs8095374	1.00[JPT][hapmap]
rs8095608	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8097521	0.84[EUR][1000 genomes]
rs9304326	0.83[EUR][1000 genomes]
rs9304327	0.83[EUR][1000 genomes]
rs9304328	0.81[EUR][1000 genomes]
rs9304329	0.96[ASN][1000 genomes]
rs9304330	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9783884	0.87[EUR][1000 genomes]
rs9783886	1.00[CEU][hapmap]
rs9783887	0.87[EUR][1000 genomes]
rs9783888	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9807399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9944637	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9945606	0.94[EUR][1000 genomes]
rs9945751	0.94[EUR][1000 genomes]
rs9946983	0.88[ASN][1000 genomes]
rs9947908	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9950562	0.84[ASN][1000 genomes]
rs9954278	0.94[EUR][1000 genomes]
rs9955853	1.00[JPT][hapmap]
rs9961065	0.87[EUR][1000 genomes]
rs9962380	0.93[EUR][1000 genomes]
rs9962458	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv962965	chr18:43678008-43706302	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Migraine - clinic-based	23793025	GWAS catalog

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43685000-43689000	Weak transcription	Gastric	stomach
2	chr18:43685000-43691200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:43685000-43693800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:43685000-43694400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:43685000-43694400	Weak transcription	Esophagus	oesophagus
6	chr18:43685000-43694400	Weak transcription	Left Ventricle	heart
7	chr18:43685000-43707000	Weak transcription	Spleen	Spleen
8	chr18:43685000-43709000	Weak transcription	Pancreas	Pancrea
9	chr18:43685200-43691000	Weak transcription	Right Atrium	heart
10	chr18:43685200-43693800	Weak transcription	Aorta	Aorta
11	chr18:43685200-43696800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:43685200-43704200	Weak transcription	Psoas Muscle	Psoas
13	chr18:43685200-43704800	Weak transcription	Placenta	Placenta
14	chr18:43685200-43709000	Weak transcription	Right Ventricle	heart
15	chr18:43685200-43712600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr18:43685200-43712600	Weak transcription	Stomach Mucosa	stomach
17	chr18:43685200-43715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr18:43685200-43735600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr18:43685400-43688600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr18:43685400-43688800	Weak transcription	Thymus	Thymus
21	chr18:43685400-43689000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr18:43685400-43689000	Weak transcription	Primary T cells from cord blood	blood
23	chr18:43685400-43689200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr18:43685400-43689200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr18:43685400-43689200	Weak transcription	Liver	Liver
26	chr18:43685400-43689600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr18:43685400-43689800	Weak transcription	Brain Angular Gyrus	brain
28	chr18:43685400-43689800	Weak transcription	Colon Smooth Muscle	Colon
29	chr18:43685400-43690400	Weak transcription	Brain Anterior Caudate	brain
30	chr18:43685400-43693200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr18:43685400-43693200	Weak transcription	Fetal Lung	lung
32	chr18:43685400-43693200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr18:43685400-43693400	Weak transcription	Brain Hippocampus Middle	brain
34	chr18:43685400-43693400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr18:43685400-43693400	Weak transcription	HSMM	muscle
36	chr18:43685400-43693600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr18:43685400-43693600	Weak transcription	NH-A	brain
38	chr18:43685400-43693800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr18:43685400-43693800	Weak transcription	Adipose Nuclei	Adipose
40	chr18:43685400-43693800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr18:43685400-43693800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr18:43685400-43693800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr18:43685400-43693800	Weak transcription	HSMMtube	muscle
44	chr18:43685400-43694200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr18:43685400-43694200	Weak transcription	NHLF	lung
46	chr18:43685400-43694400	Weak transcription	Lung	lung
47	chr18:43685400-43694400	Weak transcription	Ovary	ovary
48	chr18:43685400-43702200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr18:43685400-43702200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr18:43685400-43703600	Weak transcription	Brain Cingulate Gyrus	brain

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