Variant report

Variant	rs1392894
Chromosome Location	chr4:16510692-16510693
allele	C/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	CBX3	chr4:16510661-16511029	HCT-116	colon:	n/a	n/a
2	CTCF	chr4:16510660-16510810	NHEK	skin:	n/a	chr4:16510780-16510801
3	CTCF	chr4:16510680-16510830	GM12872	blood:	n/a	chr4:16510780-16510801
4	CTCF	chr4:16510664-16510856	HepG2	liver:	n/a	chr4:16510780-16510801
5	ZNF143	chr4:16510627-16510967	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr4:16510600-16510750	HFF-Myc	foreskin:	n/a	n/a
7	CTCF	chr4:16510660-16510810	HUVEC	blood vessel:	n/a	chr4:16510780-16510801
8	CTCF	chr4:16510628-16510922	K562	blood:	n/a	chr4:16510780-16510801
9	CTCF	chr4:16510680-16510830	GM12801	blood:	n/a	chr4:16510780-16510801
10	CBX3	chr4:16510655-16510932	K562	blood:	n/a	n/a
11	RAD21	chr4:16510675-16510934	H1-hESC	embryonic stem cell:	n/a	chr4:16510783-16510802
12	RAD21	chr4:16510546-16510986	HCT-116	colon:	n/a	chr4:16510783-16510802
13	CBX3	chr4:16510599-16510898	K562	blood:	n/a	n/a
14	CTCF	chr4:16510680-16510830	GM12878	blood:	n/a	chr4:16510780-16510801
15	CTCF	chr4:16510640-16510790	NHDF-neo	bronchial:	n/a	n/a
16	CTCF	chr4:16510680-16510830	HA-sp	spinal cord:	n/a	chr4:16510780-16510801
17	CTCF	chr4:16510680-16510830	Hela-S3	cervix:	n/a	chr4:16510780-16510801
18	CTCF	chr4:16510680-16510830	GM12866	blood:	n/a	chr4:16510780-16510801
19	KAP1	chr4:16510636-16511014	K562	blood:	n/a	n/a
20	CTCF	chr4:16510680-16510830	GM06990	blood:	n/a	chr4:16510780-16510801
21	CTCF	chr4:16510620-16510770	RPTEC	kidney:	n/a	n/a
22	CTCF	chr4:16510673-16510921	HUVEC	blood vessel:	n/a	chr4:16510780-16510801
23	CTCF	chr4:16510620-16510770	A549	lung:	n/a	n/a
24	CTCF	chr4:16510677-16510916	H1-hESC	embryonic stem cell:	n/a	chr4:16510780-16510801
25	ZNF143	chr4:16510653-16510948	K562	blood:	n/a	n/a
26	CTCF	chr4:16510680-16510830	GM12864	blood:	n/a	chr4:16510780-16510801
27	SETDB1	chr4:16510627-16510988	U2OS	brain:	n/a	n/a
28	RAD21	chr4:16510657-16510883	H1-hESC	embryonic stem cell:	n/a	chr4:16510783-16510802
29	CTCF	chr4:16510680-16510830	GM12867	blood:	n/a	chr4:16510780-16510801
30	RAD21	chr4:16510571-16511024	ECC-1	luminal epithelium:	n/a	chr4:16510783-16510802
31	CTCF	chr4:16510660-16510810	GM12865	blood:	n/a	chr4:16510780-16510801
32	CTCF	chr4:16510680-16510830	HRE	kidney:	n/a	chr4:16510780-16510801
33	CTCF	chr4:16510625-16510972	IMR90	lung:	n/a	chr4:16510780-16510801
34	CTCF	chr4:16510680-16510830	NHDF-neo	bronchial:	n/a	chr4:16510780-16510801
35	CTCF	chr4:16510660-16510810	HCM	heart:	n/a	chr4:16510780-16510801
36	CTCF	chr4:16510660-16510810	GM06990	blood:	n/a	chr4:16510780-16510801
37	RAD21	chr4:16510665-16510913	H1-hESC	embryonic stem cell:	n/a	chr4:16510783-16510802
38	CTCF	chr4:16510660-16510810	BJ	skin:	n/a	chr4:16510780-16510801
39	CTCF	chr4:16510690-16510911	K562	blood:	n/a	chr4:16510780-16510801
40	CTCF	chr4:16510620-16510977	K562	blood:	n/a	chr4:16510780-16510801
41	CTCF	chr4:16510690-16510903	GM12878	blood:	n/a	chr4:16510780-16510801
42	CTCF	chr4:16510680-16510830	HBMEC	blood vessel:	n/a	chr4:16510780-16510801
43	CTCF	chr4:16510661-16510945	GM12878	blood:	n/a	chr4:16510780-16510801
44	CTCF	chr4:16510680-16510830	HAc	cerebellar:	n/a	chr4:16510780-16510801
45	CTCF	chr4:16510680-16510830	K562	blood:	n/a	chr4:16510780-16510801
46	TRIM28	chr4:16510637-16510928	K562	blood:	n/a	n/a
47	TRIM28	chr4:16510638-16510934	K562	blood:	n/a	n/a
48	CTCF	chr4:16510660-16510810	AG09309	skin:	n/a	chr4:16510780-16510801

Variant related genes	Relation type
LDB2	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1354079	0.82[ASN][1000 genomes]
rs1392897	0.84[ASN][1000 genomes]
rs1501141	0.90[ASN][1000 genomes]
rs3805319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6449258	0.81[ASN][1000 genomes]
rs6814110	0.82[ASN][1000 genomes]
rs872479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs976362	0.82[ASN][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	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv428755	chr4:16366311-16528135	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16498400-16513200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:16498400-16518200	Weak transcription	Brain Angular Gyrus	brain
3	chr4:16501400-16510800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:16501400-16511400	Weak transcription	Gastric	stomach
5	chr4:16502200-16510800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:16502200-16512200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:16502400-16510800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr4:16502800-16511400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:16502800-16512200	Weak transcription	Pancreas	Pancrea
10	chr4:16503000-16510800	Weak transcription	Fetal Lung	lung
11	chr4:16503000-16511200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:16503000-16511400	Weak transcription	Right Ventricle	heart
13	chr4:16503000-16513000	Weak transcription	Primary T cells from cord blood	blood
14	chr4:16503200-16510800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:16503200-16518400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:16504600-16511400	Weak transcription	Esophagus	oesophagus
17	chr4:16504600-16511600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:16505400-16513400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:16505400-16522200	Weak transcription	Lung	lung
20	chr4:16505800-16512000	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:16506400-16514600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:16507400-16511400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:16508200-16510800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:16508200-16511400	Strong transcription	Ovary	ovary
25	chr4:16508800-16510800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:16509000-16512200	Strong transcription	Osteobl	bone
27	chr4:16509200-16510800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:16509200-16511600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:16509200-16514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr4:16509600-16511600	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr4:16510000-16510800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr4:16510000-16515800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:16510200-16510800	Weak transcription	Placenta	Placenta
34	chr4:16510200-16511400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:16510200-16512000	Strong transcription	Fetal Kidney	kidney
36	chr4:16510200-16518200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:16510400-16510800	Weak transcription	Liver	Liver
38	chr4:16510400-16511400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:16510400-16511400	Weak transcription	Left Ventricle	heart
40	chr4:16510400-16511400	Weak transcription	Spleen	Spleen
41	chr4:16510400-16511800	Weak transcription	Adipose Nuclei	Adipose
42	chr4:16510400-16518200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:16510600-16510800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:16510600-16510800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
45	chr4:16510600-16511200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:16510600-16511400	Weak transcription	Fetal Stomach	stomach
47	chr4:16510600-16511800	ZNF genes & repeats	HUVEC	blood vessel
48	chr4:16510600-16512400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
49	chr4:16510600-16512400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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