Variant report

Variant	rs9949682
Chromosome Location	chr18:12999821-12999822
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	chr18:12996489..12998450-chr18:12998497..13000010,2	K562	blood:
2	chr18:12988481..12994468-chr18:12998354..13003992,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266969	Chromatin interaction
ENSG00000101639	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10221326	0.92[CHB][hapmap]
rs10221384	0.92[CEU][hapmap]
rs11080620	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11663049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12605081	0.80[CEU][hapmap]
rs12954256	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12955780	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1474043	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap]
rs1786263	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1787000	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1787008	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2902856	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs3809912	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs472702	0.89[CEU][hapmap]
rs474337	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs498685	0.89[CEU][hapmap]
rs4995995	1.00[YRI][hapmap]
rs554854	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs562151	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs565832	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs567031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs570505	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs576963	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs578208	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6505774	0.82[CEU][hapmap]
rs6505776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6505780	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs692964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7229870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7233600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7234960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7241536	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8088313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8089123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8097125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9949589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9964466	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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 miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1062413	chr18:12988947-13039941	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv543657	chr18:12988947-13039941	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9949682	CEP192	cis	Brain Pons	GTEx
rs9949682	CEP192	cis	Temporal Cortex	GTEx
rs9949682	CEP192	cis	multi-tissue	Pritchard
rs9949682	CEP192	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12992000-13000600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:12992000-13004400	Weak transcription	Esophagus	oesophagus
3	chr18:12992200-13004800	Weak transcription	Aorta	Aorta
4	chr18:12992400-13000400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:12992400-13000600	Weak transcription	Placenta	Placenta
6	chr18:12992400-13004400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr18:12992600-13000400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr18:12992600-13031200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr18:12992800-13004000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr18:12992800-13008800	Weak transcription	Colonic Mucosa	Colon
11	chr18:12992800-13009200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr18:12992800-13013200	Weak transcription	Fetal Kidney	kidney
13	chr18:12992800-13016000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr18:12993000-13001400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr18:12993000-13006400	Weak transcription	Fetal Brain Female	brain
16	chr18:12993000-13023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr18:12993200-13000200	Weak transcription	HSMM	muscle
18	chr18:12993200-13000400	Weak transcription	Adipose Nuclei	Adipose
19	chr18:12993200-13001000	Weak transcription	Fetal Intestine Large	intestine
20	chr18:12993200-13001200	Weak transcription	A549	lung
21	chr18:12993200-13004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr18:12993200-13004800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr18:12993200-13006800	Weak transcription	HSMMtube	muscle
24	chr18:12993200-13007000	Weak transcription	Brain Substantia Nigra	brain
25	chr18:12993200-13008400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:12993200-13008400	Weak transcription	Osteobl	bone
27	chr18:12993200-13008800	Weak transcription	NHLF	lung
28	chr18:12993400-13000200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr18:12993400-13000200	Weak transcription	Liver	Liver
30	chr18:12993400-13000200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr18:12993400-13000200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:12993400-13000600	Weak transcription	Fetal Stomach	stomach
33	chr18:12993400-13000800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr18:12993400-13003000	Weak transcription	Fetal Muscle Leg	muscle
35	chr18:12993400-13003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr18:12993400-13006200	Weak transcription	NH-A	brain
37	chr18:12993400-13006600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr18:12993400-13008200	Weak transcription	Brain Angular Gyrus	brain
39	chr18:12993400-13017800	Weak transcription	Stomach Mucosa	stomach
40	chr18:12993600-13000200	Weak transcription	Primary B cells from cord blood	blood
41	chr18:12993600-13000200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr18:12993600-13000400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr18:12993600-13000400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:12993600-13000400	Weak transcription	Lung	lung
45	chr18:12993600-13001800	Weak transcription	Brain Germinal Matrix	brain
46	chr18:12993600-13003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr18:12993600-13011800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12993600-13011800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr18:12993800-13000000	Weak transcription	Thymus	Thymus
50	chr18:12993800-13000400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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