Variant report

Variant	rs7007246
Chromosome Location	chr8:6312223-6312224
allele	G/T
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	FOXM1	chr8:6311787-6312301	GM12878	blood:	n/a	n/a
2	MTA3	chr8:6311707-6312390	GM12878	blood:	n/a	n/a
3	IRF4	chr8:6311797-6312315	GM12878	blood:	n/a	n/a
4	MEF2A	chr8:6311957-6312248	GM12878	blood:	n/a	n/a
5	BCL11A	chr8:6311822-6312292	GM12878	blood:	n/a	n/a
6	EP300	chr8:6311936-6312267	GM12878	blood:	n/a	chr8:6312044-6312054
7	NFIC	chr8:6311751-6312308	GM12878	blood:	n/a	n/a
8	RUNX3	chr8:6311811-6312323	GM12878	blood:	n/a	n/a
9	EBF1	chr8:6311827-6312237	GM12878	blood:	n/a	n/a
10	CEBPB	chr8:6311794-6312224	IMR90	lung:	n/a	n/a
11	ATF2	chr8:6311778-6312314	GM12878	blood:	n/a	n/a
12	MEF2A	chr8:6311795-6312323	GM12878	blood:	n/a	n/a
13	BATF	chr8:6311851-6312262	GM12878	blood:	n/a	chr8:6312030-6312040 chr8:6312029-6312040
14	RUNX3	chr8:6311731-6312376	GM12878	blood:	n/a	n/a
15	NFIC	chr8:6311781-6312382	GM12878	blood:	n/a	n/a
16	NFATC1	chr8:6311797-6312321	GM12878	blood:	n/a	n/a
17	POLR2A	chr8:6311968-6312324	A549	lung:	n/a	n/a
18	BATF	chr8:6311806-6312285	GM12878	blood:	n/a	chr8:6312030-6312040 chr8:6312029-6312040

Variant related genes	Relation type
MCPH1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2166010	1.00[ASW][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.86[AFR][1000 genomes]
rs2979668	1.00[MEX][hapmap]
rs41313954	0.81[AFR][1000 genomes]
rs58520213	1.00[AMR][1000 genomes]
rs73516751	0.82[AFR][1000 genomes]
rs73516761	1.00[AMR][1000 genomes]
rs73518723	1.00[AMR][1000 genomes]
rs73518764	1.00[AMR][1000 genomes]
rs73518770	1.00[AMR][1000 genomes]
rs73520655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73520669	1.00[AMR][1000 genomes]
rs7817926	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs7841259	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7844807	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890034	chr8:5926632-6427868	Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1021175	chr8:5965453-6880364	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1027682	chr8:6018123-6920312	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3506199	chr8:6116693-6536592	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
5	esv3506200	chr8:6116693-6536592	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats 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	11 gene(s)	inside rSNPs	diseases
6	nsv933107	chr8:6173244-6312807	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv482828	chr8:6182711-6355710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv890055	chr8:6237397-6351252	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv933282	chr8:6261036-6440592	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1015981	chr8:6286575-6578450	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1027313	chr8:6286575-6920312	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7007246	NEURL1B	trans	lymphoblastoid	seeQTL
rs7007246	FAM90A5	cis	lymphoblastoid	seeQTL
rs7007246	ABP1	trans	lymphoblastoid	seeQTL
rs7007246	VWDE	trans	lymphoblastoid	seeQTL
rs7007246	TDO2	trans	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:6265000-6339200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr8:6282800-6313400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:6287600-6344400	Weak transcription	Small Intestine	intestine
4	chr8:6301000-6338400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr8:6302800-6313800	Weak transcription	Brain Angular Gyrus	brain
6	chr8:6302800-6339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:6303000-6312400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr8:6303000-6313400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr8:6303000-6313800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr8:6303000-6317200	Weak transcription	Brain Substantia Nigra	brain
11	chr8:6303000-6317800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr8:6303000-6319400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr8:6303000-6321000	Weak transcription	Psoas Muscle	Psoas
14	chr8:6303000-6321000	Weak transcription	Hela-S3	cervix
15	chr8:6303000-6322800	Weak transcription	Ovary	ovary
16	chr8:6303000-6322800	Weak transcription	Spleen	Spleen
17	chr8:6303000-6325000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr8:6303000-6325200	Weak transcription	Pancreas	Pancrea
19	chr8:6303000-6338200	Weak transcription	Gastric	stomach
20	chr8:6303000-6338200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr8:6303000-6338400	Weak transcription	Colonic Mucosa	Colon
22	chr8:6303000-6338400	Weak transcription	Right Ventricle	heart
23	chr8:6303000-6339400	Weak transcription	Placenta	Placenta
24	chr8:6303200-6316800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr8:6303200-6318200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr8:6303200-6318800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr8:6303200-6320400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr8:6303200-6321000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr8:6303200-6322600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr8:6303200-6322800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr8:6303200-6339400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr8:6303200-6339400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr8:6303200-6340000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr8:6303400-6312400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:6303400-6313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr8:6303400-6314600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr8:6303400-6320600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr8:6303400-6320800	Weak transcription	Colon Smooth Muscle	Colon
39	chr8:6303400-6321000	Weak transcription	Brain Anterior Caudate	brain
40	chr8:6303400-6321200	Weak transcription	HUVEC	blood vessel
41	chr8:6303600-6321600	Weak transcription	Brain Germinal Matrix	brain
42	chr8:6303800-6338400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr8:6304000-6313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr8:6304000-6322600	Weak transcription	Fetal Brain Female	brain
45	chr8:6304000-6338000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr8:6304400-6318200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr8:6304400-6360200	Weak transcription	Esophagus	oesophagus
48	chr8:6304600-6313400	Weak transcription	Fetal Intestine Small	intestine
49	chr8:6304600-6313800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr8:6304600-6317400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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