Variant report

Variant	rs10148712
Chromosome Location	chr14:39647406-39647407
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:39647281-39648417	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr14:39647367-39647732	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr14:39642960-39651251	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr14:39647352-39647652	K562	blood:	n/a	n/a
5	POLR2A	chr14:39647316-39647636	Hela-S3	cervix:	n/a	n/a
6	HEY1	chr14:39646033-39648837	HepG2	liver:	n/a	n/a
7	POLR2A	chr14:39647312-39647912	GM12878	blood:	n/a	n/a
8	POLR2A	chr14:39647365-39647912	GM12892	blood:	n/a	n/a
9	HEY1	chr14:39645676-39647521	HepG2	liver:	n/a	n/a
10	POLR2A	chr14:39643051-39648902	HepG2	liver:	n/a	n/a
11	POLR2A	chr14:39645641-39647605	HepG2	liver:	n/a	n/a
12	POLR2A	chr14:39647321-39647580	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr14:39647354-39648404	HepG2	liver:	n/a	n/a
14	POLR2A	chr14:39643261-39648811	K562	blood:	n/a	n/a
15	POLR2A	chr14:39647197-39648901	GM12878	blood:	n/a	n/a
16	POLR2A	chr14:39647406-39648190	K562	blood:	n/a	n/a
17	POLR2A	chr14:39647391-39647904	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr14:39647370-39648850	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39643730..39648156-chr14:39734640..39738499,10	MCF-7	breast:
2	chr14:39647303..39649184-chr14:39736283..39738077,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259083	TF binding region
PNN	TF binding region
ENSG00000258940	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000258941	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1002193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129762	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10131369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10134166	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10134656	0.82[AMR][1000 genomes]
rs10135561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136637	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10140763	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10141081	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs10141924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142117	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10142350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145010	1.00[YRI][hapmap]
rs10145417	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10146176	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1040680	0.83[AMR][1000 genomes]
rs10483542	0.82[JPT][hapmap]
rs1050136	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs11622731	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11622968	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11623907	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs11623945	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs11624584	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11626002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11627264	0.82[AMR][1000 genomes]
rs11628564	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs11628784	0.84[ASN][1000 genomes]
rs11848067	0.82[AMR][1000 genomes]
rs11849209	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11850579	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11851680	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587208	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379129	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17092044	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17092050	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17108696	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs17108948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144528	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs2273592	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277458	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs28414518	0.82[AMR][1000 genomes]
rs28437577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28470602	0.82[AMR][1000 genomes]
rs28501673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583114	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28666016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28701960	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28821293	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3759544	0.82[JPT][hapmap]
rs45622837	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55737943	0.82[AMR][1000 genomes]
rs56064304	0.82[AMR][1000 genomes]
rs56105133	0.82[AMR][1000 genomes]
rs57326310	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57482489	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57555422	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58601678	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59465524	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7144625	0.82[AMR][1000 genomes]
rs7155307	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7156264	0.81[CHB][hapmap]
rs74048710	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74048711	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs761805	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8018720	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs926970	0.82[AMR][1000 genomes]
rs926971	0.82[JPT][hapmap]
rs993675	0.82[AMR][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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10148712	SEC23A	cis	parietal	SCAN
rs10148712	CTAGE5	cis	parietal	SCAN
rs10148712	PNN	cis	lymphoblastoid	seeQTL
rs10148712	EAPP	cis	cerebellum	SCAN
rs10148712	BRMS1L	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39645400-39647600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
2	chr14:39645400-39648000	Weak transcription	Fetal Brain Male	brain
3	chr14:39645400-39649000	Genic enhancers	Primary T cells fromperipheralblood	blood
4	chr14:39645600-39655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr14:39645800-39648200	Strong transcription	Lung	lung
6	chr14:39645800-39648600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:39645800-39651200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr14:39645800-39653000	Strong transcription	Placenta Amnion	Placenta Amnion
9	chr14:39645800-39653400	Strong transcription	H9 Cell Line	embryonic stem cell
10	chr14:39645800-39654600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr14:39645800-39655200	Strong transcription	Placenta	Placenta
12	chr14:39645800-39657200	Strong transcription	HSMM	muscle
13	chr14:39646000-39651400	Strong transcription	Fetal Kidney	kidney
14	chr14:39646000-39652800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr14:39646000-39654200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:39646000-39654800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr14:39646000-39654800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr14:39646000-39655200	Strong transcription	HSMMtube	muscle
19	chr14:39646200-39647800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:39646200-39648800	Strong transcription	Ovary	ovary
21	chr14:39646200-39651000	Strong transcription	Esophagus	oesophagus
22	chr14:39646200-39651600	Genic enhancers	HUVEC	blood vessel
23	chr14:39646200-39652600	Strong transcription	Brain Anterior Caudate	brain
24	chr14:39646200-39653000	Strong transcription	Fetal Lung	lung
25	chr14:39646200-39654400	Strong transcription	Primary B cells from cord blood	blood
26	chr14:39646200-39654400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr14:39646200-39654400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr14:39646200-39654600	Strong transcription	Osteobl	bone
29	chr14:39646200-39654800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:39646200-39654800	Strong transcription	Fetal Brain Female	brain
31	chr14:39646200-39655000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr14:39646400-39647600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr14:39646400-39647800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr14:39646400-39648000	Strong transcription	Psoas Muscle	Psoas
35	chr14:39646400-39648400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr14:39646400-39648800	Strong transcription	Spleen	Spleen
37	chr14:39646400-39648800	Genic enhancers	A549	lung
38	chr14:39646400-39649000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr14:39646400-39649400	Weak transcription	Fetal Heart	heart
40	chr14:39646400-39649600	Weak transcription	Stomach Mucosa	stomach
41	chr14:39646400-39649800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr14:39646400-39649800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:39646400-39650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr14:39646400-39651200	Strong transcription	Colonic Mucosa	Colon
45	chr14:39646400-39651200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr14:39646400-39652600	Strong transcription	Brain Hippocampus Middle	brain
47	chr14:39646400-39653000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:39646400-39653000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr14:39646400-39653400	Strong transcription	NHDF-Ad	bronchial
50	chr14:39646400-39654200	Strong transcription	Brain Substantia Nigra	brain

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