Variant report

Variant	rs12019258
Chromosome Location	chr4:141918200-141918201
allele	A/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	CTCF	chr4:141918080-141918230	RPTEC	kidney:	n/a	n/a
2	CTCF	chr4:141918080-141918230	NHDF-neo	bronchial:	n/a	n/a
3	CTCF	chr4:141918160-141918310	HA-sp	spinal cord:	n/a	n/a
4	CTCF	chr4:141918060-141918210	HCPEpiC	choroid plexus:	n/a	n/a
5	CTCF	chr4:141918140-141918290	AG09309	skin:	n/a	n/a
6	CTCF	chr4:141918120-141918270	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr4:141918180-141918330	HRPEpiC	eye:	n/a	n/a
8	CTCF	chr4:141918195-141918233	K562	blood:	n/a	n/a
9	CTCF	chr4:141918100-141918250	AG04450	lung:	n/a	n/a
10	CTCF	chr4:141918174-141918232	K562	blood:	n/a	n/a
11	STAT3	chr4:141918008-141918208	MCF10A-Er-Src	breast:	n/a	chr4:141918142-141918151 chr4:141918143-141918152 chr4:141918140-141918154
12	CTCF	chr4:141918108-141918267	Kidney_OC	kidney:	n/a	n/a
13	TEAD4	chr4:141917894-141918328	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr4:141918100-141918250	HRPEpiC	eye:	n/a	n/a
15	CTCF	chr4:141918100-141918250	HRE	kidney:	n/a	n/a
16	CTCF	chr4:141918120-141918270	BE2_C	brain:	n/a	n/a
17	CTCF	chr4:141918120-141918270	HPF	lung:	n/a	n/a
18	STAT3	chr4:141917978-141918277	MCF10A-Er-Src	breast:	n/a	chr4:141918142-141918151 chr4:141918143-141918152 chr4:141918140-141918154
19	RAD21	chr4:141917983-141918384	IMR90	lung:	n/a	n/a
20	CTCF	chr4:141917981-141918412	IMR90	lung:	n/a	n/a
21	STAT3	chr4:141918015-141918296	MCF10A-Er-Src	breast:	n/a	chr4:141918142-141918151 chr4:141918143-141918152 chr4:141918140-141918154
22	CTCF	chr4:141918080-141918230	HPAF	blood vessel:	n/a	n/a
23	CTCF	chr4:141918060-141918210	NHEK	skin:	n/a	n/a
24	CTCF	chr4:141918120-141918270	AG10803	skin:	n/a	n/a
25	CTCF	chr4:141918080-141918230	HMF	breast:	n/a	n/a
26	CTCF	chr4:141918140-141918290	AG09319	gingival:	n/a	n/a
27	CTCF	chr4:141918138-141918292	Medullo	brain:	n/a	n/a
28	MAX	chr4:141917757-141918287	ECC-1	luminal epithelium:	n/a	n/a
29	RAD21	chr4:141918177-141918255	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr4:141918100-141918250	RPTEC	kidney:	n/a	n/a
31	CTCF	chr4:141918140-141918290	HRE	kidney:	n/a	n/a
32	CTCF	chr4:141918120-141918270	NHEK	skin:	n/a	n/a
33	MAFK	chr4:141918025-141918322	IMR90	lung:	n/a	n/a
34	CTCF	chr4:141918200-141918350	HFF	foreskin:	n/a	n/a
35	CTCF	chr4:141918160-141918310	HAc	cerebellar:	n/a	n/a
36	CTCF	chr4:141918080-141918230	AG09319	gingival:	n/a	n/a
37	MAX	chr4:141917840-141918283	ECC-1	luminal epithelium:	n/a	n/a
38	CTCF	chr4:141918140-141918290	AG04449	skin:	n/a	n/a
39	RAD21	chr4:141918075-141918319	SK-N-SH_RA	brain:	n/a	n/a
40	CTCF	chr4:141918140-141918290	HA-sp	spinal cord:	n/a	n/a
41	TEAD4	chr4:141917872-141918357	ECC-1	luminal epithelium:	n/a	n/a
42	CTCF	chr4:141918100-141918250	AG09309	skin:	n/a	n/a
43	CTCF	chr4:141918120-141918270	AG04449	skin:	n/a	n/a
44	CTCF	chr4:141918180-141918330	AG10803	skin:	n/a	n/a
45	CTCF	chr4:141918100-141918250	BJ	skin:	n/a	n/a
46	STAT3	chr4:141918020-141918326	MCF10A-Er-Src	breast:	n/a	chr4:141918142-141918151 chr4:141918143-141918152 chr4:141918140-141918154
47	NR3C1	chr4:141917839-141918242	ECC-1	luminal epithelium:	n/a	n/a
48	CTCF	chr4:141918120-141918270	HCFaa	heart:	n/a	n/a
49	CTCF	chr4:141918140-141918290	HCPEpiC	choroid plexus:	n/a	n/a

Variant related genes	Relation type
RNF150	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1003257	0.93[EUR][1000 genomes]
rs11932554	0.92[EUR][1000 genomes]
rs13129199	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1364881	0.93[EUR][1000 genomes]
rs1425445	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17340802	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17343501	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17425151	0.93[EUR][1000 genomes]
rs1895762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445273	1.00[ASN][1000 genomes]
rs3851424	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3851425	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56288735	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59074378	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60293572	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62325721	0.93[EUR][1000 genomes]
rs62325722	0.93[EUR][1000 genomes]
rs62325723	0.93[EUR][1000 genomes]
rs62326020	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62326022	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62326024	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6537024	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6823670	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73849462	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7665647	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7690780	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7692524	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9994743	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830090	chr4:141770494-141947764	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830091	chr4:141796603-141980546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:141910600-141919600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:141911000-141923600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:141913800-141919400	Weak transcription	Right Ventricle	heart
4	chr4:141914000-141919200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:141914200-141920200	Weak transcription	Lung	lung
6	chr4:141914800-141918600	Enhancers	Colon Smooth Muscle	Colon
7	chr4:141915400-141919400	Weak transcription	Right Atrium	heart
8	chr4:141915600-141919600	Weak transcription	Aorta	Aorta
9	chr4:141915600-141919600	Weak transcription	Psoas Muscle	Psoas
10	chr4:141915800-141919200	Enhancers	Fetal Heart	heart
11	chr4:141916000-141919800	Weak transcription	Fetal Stomach	stomach
12	chr4:141916800-141919400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:141916800-141919400	Weak transcription	Fetal Muscle Leg	muscle
14	chr4:141916800-141919400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr4:141916800-141919400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:141916800-141919600	Weak transcription	Left Ventricle	heart
17	chr4:141916800-141919600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:141916800-141919600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:141916800-141919800	Weak transcription	Ovary	ovary
20	chr4:141917200-141918200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:141917200-141923400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:141917600-141918200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:141917600-141918200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:141917600-141918400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:141917600-141918600	Enhancers	Osteobl	bone
26	chr4:141917800-141918200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:141917800-141923400	Weak transcription	Adipose Nuclei	Adipose
28	chr4:141918000-141918400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr4:141918200-141919400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:141918200-141923400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:141918200-141923400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:141918200-141923400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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