Variant report

Variant	rs3790512
Chromosome Location	chr1:151680974-151680975
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	POLR2A	chr1:151680966-151683349	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151582188..151584894-chr1:151679011..151681614,2	MCF-7	breast:
2	chr1:151680360..151683089-chr1:151739535..151742461,2	MCF-7	breast:
3	chr1:151672629..151675087-chr1:151680419..151682673,2	K562	blood:
4	chr1:151680409..151681994-chr1:151800376..151802986,2	K562	blood:

Variant related genes	Relation type
CELF3	TF binding region
RIIAD1	TF binding region
ENSG00000240510	TF binding region
ENSG00000143376	Chromatin interaction
ENSG00000249602	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000227045	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1048694	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204866	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11586679	0.81[EUR][1000 genomes]
rs1196350	0.84[MKK][hapmap]
rs1196352	0.92[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1196357	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs1196459	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196464	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1196465	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1201651	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1211981	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1308137	0.88[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1308139	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1308143	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1308145	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1308146	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1308147	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1308148	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1308152	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1308158	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1717128	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17641780	0.84[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1781434	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1891589	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs2460996	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2489892	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2495392	0.92[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2495393	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2495394	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3204344	0.88[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs6684548	0.85[EUR][1000 genomes]
rs6685067	0.88[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6687866	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs6702842	0.87[CEU][hapmap];0.91[TSI][hapmap]
rs7534887	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3790512	PLEKHO1	cis	cerebellum	SCAN
rs3790512	LCE1C	cis	parietal	SCAN
rs3790512	LINGO4	cis	cerebellum	SCAN
rs3790512	LYSMD1	cis	parietal	SCAN
rs3790512	TDRKH	cis	parietal	SCAN
rs3790512	TDRKH	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151663200-151683200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:151666000-151685400	Weak transcription	A549	lung
3	chr1:151667000-151687400	Weak transcription	K562	blood
4	chr1:151667800-151686000	Weak transcription	HMEC	breast
5	chr1:151669600-151681200	Strong transcription	Fetal Brain Female	brain
6	chr1:151670000-151689800	Weak transcription	Pancreas	Pancrea
7	chr1:151671400-151682600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:151672400-151684800	Weak transcription	Small Intestine	intestine
9	chr1:151673800-151682400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:151673800-151685200	Weak transcription	Fetal Kidney	kidney
11	chr1:151674000-151682400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:151674000-151685400	Weak transcription	Gastric	stomach
13	chr1:151674200-151683200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:151674200-151683200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:151674200-151687400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:151674600-151681800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:151674600-151682400	Weak transcription	Brain Substantia Nigra	brain
18	chr1:151674600-151682600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:151674600-151683200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:151674600-151683200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:151674600-151685200	Weak transcription	Fetal Lung	lung
22	chr1:151674600-151686000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:151674800-151681800	Weak transcription	Brain Angular Gyrus	brain
24	chr1:151674800-151686200	Weak transcription	Esophagus	oesophagus
25	chr1:151675400-151681400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:151675800-151681000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:151676200-151682400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:151677000-151681800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:151678000-151682000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:151679000-151682000	Weak transcription	Brain Anterior Caudate	brain
31	chr1:151679200-151682200	Strong transcription	Brain Germinal Matrix	brain
32	chr1:151679200-151684600	Weak transcription	Colonic Mucosa	Colon
33	chr1:151679400-151681000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:151679400-151684400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:151679600-151681800	Strong transcription	Fetal Intestine Small	intestine
36	chr1:151679600-151684000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:151679600-151684800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:151680200-151681400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:151680200-151685400	Weak transcription	Spleen	Spleen
40	chr1:151680200-151687400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:151680400-151681200	Genic enhancers	Fetal Intestine Large	intestine
42	chr1:151680400-151684400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:151680400-151684600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:151680600-151683000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:151680800-151682000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:151680800-151686800	Enhancers	Fetal Brain Male	brain

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