Variant report

Variant	rs12511253
Chromosome Location	chr4:54363801-54363802
allele	A/G
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	CTCF	chr4:54363740-54363890	HAc	cerebellar:	n/a	n/a
2	CTCF	chr4:54363800-54363950	HMF	breast:	n/a	n/a
3	CTCF	chr4:54363800-54363950	AG10803	skin:	n/a	n/a
4	CTCF	chr4:54363800-54363950	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr4:54363760-54363910	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr4:54363740-54363890	Caco-2	colon:	n/a	n/a
7	CTCF	chr4:54363760-54363910	HCM	heart:	n/a	n/a
8	CTCF	chr4:54363740-54363890	AG04450	lung:	n/a	n/a
9	CTCF	chr4:54363780-54363930	HMEC	breast:	n/a	n/a
10	CTCF	chr4:54363760-54363910	HFF-Myc	foreskin:	n/a	n/a
11	CTCF	chr4:54363740-54363890	NHDF-neo	bronchial:	n/a	n/a
12	CTCF	chr4:54363760-54363910	HA-sp	spinal cord:	n/a	n/a
13	CTCF	chr4:54363760-54363910	NHDF-neo	bronchial:	n/a	n/a
14	RCOR1	chr4:54363668-54364010	HepG2	liver:	n/a	n/a
15	CTCF	chr4:54363780-54363930	HPF	lung:	n/a	n/a
16	SMC3	chr4:54363708-54363958	HepG2	liver:	n/a	n/a
17	CEBPB	chr4:54363695-54363879	HepG2	liver:	n/a	chr4:54363823-54363834
18	CTCF	chr4:54363760-54363910	Caco-2	colon:	n/a	n/a
19	CEBPB	chr4:54363664-54364003	IMR90	lung:	n/a	chr4:54363823-54363834
20	SMC3	chr4:54363758-54363828	Hela-S3	cervix:	n/a	n/a
21	CTCF	chr4:54363760-54363910	HCPEpiC	choroid plexus:	n/a	n/a
22	CTCF	chr4:54363760-54363910	AG10803	skin:	n/a	n/a
23	CTCF	chr4:54363800-54363950	HMEC	breast:	n/a	n/a
24	CEBPB	chr4:54363673-54363994	H1-hESC	embryonic stem cell:	n/a	chr4:54363823-54363834
25	CTCF	chr4:54363800-54363950	HFF	foreskin:	n/a	n/a
26	CTCF	chr4:54363800-54363950	AoAF	blood vessel:	n/a	n/a
27	CTCF	chr4:54363800-54363950	BJ	skin:	n/a	n/a
28	CTCF	chr4:54363760-54363910	AG09319	gingival:	n/a	n/a
29	CEBPB	chr4:54363688-54363983	Hela-S3	cervix:	n/a	chr4:54363823-54363834
30	CTCF	chr4:54363740-54363890	AG09309	skin:	n/a	n/a
31	CTCF	chr4:54363720-54363870	AG09309	skin:	n/a	n/a
32	RAD21	chr4:54363702-54363971	IMR90	lung:	n/a	chr4:54363854-54363861
33	TEAD4	chr4:54363683-54364001	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr4:54363797-54363854	HepG2	liver:	n/a	n/a
35	CTCF	chr4:54363740-54363890	HPF	lung:	n/a	n/a
36	CTCF	chr4:54363780-54363930	HCPEpiC	choroid plexus:	n/a	n/a
37	CTCF	chr4:54363780-54363930	AG04449	skin:	n/a	n/a
38	CTCF	chr4:54363692-54364007	IMR90	lung:	n/a	n/a
39	CEBPB	chr4:54363648-54364018	HepG2	liver:	n/a	chr4:54363823-54363834
40	CTCF	chr4:54363740-54363890	AoAF	blood vessel:	n/a	n/a
41	TBP	chr4:54363556-54363949	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr4:54363780-54363930	AG04450	lung:	n/a	n/a

Variant related genes	Relation type
LNX1-AS1	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10001201	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs10005424	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10007903	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10011259	0.81[CEU][hapmap]
rs10011394	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10028142	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10032903	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11133276	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11722866	0.85[EUR][1000 genomes]
rs11723755	0.85[EUR][1000 genomes]
rs11725230	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs11734039	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11734681	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12507563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507739	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12508701	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12511088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12651390	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs13150384	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1481819	0.81[CEU][hapmap]
rs1481824	0.81[CEU][hapmap]
rs1531748	0.85[CEU][hapmap]
rs17082893	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17082923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17520800	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2090117	0.81[CEU][hapmap]
rs2271558	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412447	0.82[CEU][hapmap]
rs2412488	0.81[CEU][hapmap]
rs28414913	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35089837	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35978987	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36011216	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3765158	0.81[CEU][hapmap]
rs3811785	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs4864760	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs4864766	0.82[YRI][hapmap]
rs4864767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57297394	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554104	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs6554105	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6554106	0.81[CEU][hapmap]
rs6818788	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6822201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825364	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6828559	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6832626	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833766	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[EUR][1000 genomes]
rs6838260	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840343	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843529	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682199	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7686876	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs7688853	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689981	0.84[EUR][1000 genomes]
rs7690908	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7691578	0.85[EUR][1000 genomes]
rs7691892	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7698792	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs931181	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs931182	0.82[CEU][hapmap]
rs9312639	0.90[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9995284	0.82[EUR][1000 genomes]
rs9996883	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54329600-54373600	Weak transcription	Brain Germinal Matrix	brain
2	chr4:54329800-54374000	Weak transcription	Left Ventricle	heart
3	chr4:54333000-54374800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
5	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:54343600-54364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:54346400-54374000	Weak transcription	Right Ventricle	heart
8	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
10	chr4:54356600-54373400	Weak transcription	Right Atrium	heart
11	chr4:54358600-54365400	Weak transcription	Lung	lung
12	chr4:54361400-54364600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:54361800-54364000	Strong transcription	Fetal Intestine Small	intestine
14	chr4:54362000-54366600	Enhancers	Ovary	ovary
15	chr4:54362400-54374200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:54362600-54364600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:54362600-54368000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr4:54362800-54365200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:54362800-54365200	Enhancers	Fetal Lung	lung
20	chr4:54362800-54366600	Enhancers	Fetal Muscle Leg	muscle
21	chr4:54362800-54373000	Weak transcription	Liver	Liver
22	chr4:54362800-54376000	Weak transcription	Brain Angular Gyrus	brain
23	chr4:54363000-54364000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:54363000-54364200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:54363000-54364200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:54363000-54364200	Enhancers	Adipose Nuclei	Adipose
27	chr4:54363200-54364000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:54363200-54364200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr4:54363200-54364400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:54363200-54364400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:54363200-54366200	Weak transcription	Pancreas	Pancrea
32	chr4:54363200-54373400	Weak transcription	Gastric	stomach
33	chr4:54363200-54384200	Weak transcription	Esophagus	oesophagus
34	chr4:54363400-54364200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr4:54363400-54364200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:54363400-54364200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr4:54363400-54364200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:54363400-54364200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr4:54363400-54364200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:54363400-54364200	Enhancers	Placenta	Placenta
41	chr4:54363400-54364400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr4:54363400-54364400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr4:54363400-54365400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:54363400-54365400	Enhancers	Fetal Stomach	stomach
45	chr4:54363400-54366800	Enhancers	HSMMtube	muscle
46	chr4:54363600-54364000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr4:54363600-54364000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:54363600-54364000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:54363600-54364000	Enhancers	Fetal Muscle Trunk	muscle
50	chr4:54363600-54364000	Enhancers	Placenta Amnion	Placenta Amnion

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