Variant report

Variant	rs12751350
Chromosome Location	chr1:151550673-151550674
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151549985..151552778-chr1:151557616..151559684,2	MCF-7	breast:
2	1:151496437-151509688..1:151546427-151553405	Hela-S3	cervix:
3	chr1:151549087..151552295-chr1:151579604..151582437,3	MCF-7	breast:
4	1:151270864-151283078..1:151546427-151553405	K562	blood:
5	chr1:151547303..151551460-chr1:151552210..151554912,4	K562	blood:
6	chr1:151508189..151514847-chr1:151547303..151553587,9	MCF-7	breast:
7	1:151516085-151535167..1:151546427-151553405	GM12878	blood:
8	1:151512437-151516085..1:151546427-151553405	Hela-S3	cervix:
9	chr1:151544037..151547863-chr1:151548190..151551893,4	K562	blood:
10	chr1:151550211..151552157-chr1:151552278..151554643,2	MCF-7	breast:
11	1:151254384-151268403..1:151546427-151553405	GM12878	blood:
12	chr1:151545407..151547863-chr1:151548190..151551142,2	K562	blood:
13	1:151426875-151427826..1:151546427-151553405	Hela-S3	cervix:
14	1:151219411-151234038..1:151546427-151553405	GM12878	blood:
15	chr1:151549748..151551460-chr1:151553412..151555994,2	K562	blood:
16	1:151203965-151215310..1:151546427-151553405	GM12878	blood:
17	1:151427826-151434310..1:151546427-151553405	Hela-S3	cervix:
18	1:151411623-151426875..1:151546427-151553405	GM12878	blood:
19	1:151368336-151375897..1:151546427-151553405	GM12878	blood:
20	1:151309061-151322694..1:151546427-151553405	Hela-S3	cervix:
21	1:151546427-151553405..1:151618750-151636526	GM12878	blood:

No data

Variant related genes	Relation type
ENSG00000265753	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000237976	Chromatin interaction
ENSG00000143390	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000207606	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000252840	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10218788	0.92[EUR][1000 genomes]
rs10494267	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11807809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12090862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12564097	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12723898	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12734011	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12734511	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12747024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747990	0.91[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1891592	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1935886	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34180474	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34690266	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3748608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3748610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970919	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6587605	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675022	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6679183	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6691958	0.95[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6698282	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6704177	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7554707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12751350	FLG2	cis	cerebellum	SCAN
rs12751350	TUFT1	cis	parietal	SCAN
rs12751350	MRPS21	cis	parietal	SCAN
rs12751350	OAZ3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151514400-151556800	Weak transcription	Fetal Brain Male	brain
2	chr1:151521800-151559000	Weak transcription	Small Intestine	intestine
3	chr1:151532600-151551200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:151533000-151557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:151533800-151561600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:151535800-151561800	Weak transcription	Brain Substantia Nigra	brain
7	chr1:151537000-151556800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:151537400-151556000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:151537400-151558400	Weak transcription	Fetal Kidney	kidney
10	chr1:151538000-151557400	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:151539000-151556400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:151539000-151557000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:151539600-151555400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:151541000-151552600	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:151541000-151553200	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:151541200-151557000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:151541400-151556400	Strong transcription	Fetal Stomach	stomach
18	chr1:151542000-151557000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:151542600-151557400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:151542800-151556600	Strong transcription	Fetal Intestine Small	intestine
21	chr1:151542800-151556600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:151543800-151556400	Strong transcription	Fetal Intestine Large	intestine
23	chr1:151544800-151552000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:151545200-151555000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:151545200-151556600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:151545800-151553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:151546400-151555200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:151546600-151552800	Strong transcription	Colon Smooth Muscle	Colon
29	chr1:151547400-151553200	Weak transcription	Brain Angular Gyrus	brain
30	chr1:151547400-151556000	Weak transcription	Spleen	Spleen
31	chr1:151547600-151550800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:151547600-151551000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:151547600-151551400	Strong transcription	HSMMtube	muscle
34	chr1:151547600-151551800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:151547600-151551800	Weak transcription	Colonic Mucosa	Colon
36	chr1:151547600-151556200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:151547600-151556200	Weak transcription	HUVEC	blood vessel
38	chr1:151547800-151551200	Weak transcription	Right Ventricle	heart
39	chr1:151547800-151551600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:151548000-151551200	Weak transcription	Left Ventricle	heart
41	chr1:151548000-151551200	Weak transcription	HMEC	breast
42	chr1:151548000-151551400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:151548000-151551800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:151548000-151551800	Weak transcription	NHDF-Ad	bronchial
45	chr1:151548000-151552200	Weak transcription	NHLF	lung
46	chr1:151548000-151552400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:151548000-151555000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:151548000-151556200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:151548000-151556800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:151548000-151557200	Weak transcription	Brain Inferior Temporal Lobe	brain

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