Variant report

Variant	rs17037232
Chromosome Location	chr4:159093958-159093959
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:97)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:97 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:159093820-159093970	GM12873	blood:	n/a	n/a
2	MAFK	chr4:159093854-159094006	K562	blood:	n/a	n/a
3	FOXA2	chr4:159093763-159094019	HepG2	liver:	n/a	n/a
4	RAD21	chr4:159093493-159094270	HCT-116	colon:	n/a	n/a
5	RAD21	chr4:159093381-159094105	HCT-116	colon:	n/a	n/a
6	CTCF	chr4:159093732-159093959	GM13977	blood:	n/a	n/a
7	ZNF143	chr4:159093691-159094005	GM12878	blood:	n/a	n/a
8	MYC	chr4:159093869-159094054	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr4:159093228-159093996	MCF10A-Er-Src	breast:	n/a	n/a
10	CTCF	chr4:159093365-159094252	A549	lung:	n/a	n/a
11	HNF4G	chr4:159093740-159094055	HepG2	liver:	n/a	n/a
12	RAD21	chr4:159093500-159094111	MCF-7	breast:	n/a	n/a
13	POLR2A	chr4:159093880-159094005	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr4:159093693-159094122	K562	blood:	n/a	n/a
15	RAD21	chr4:159093426-159094080	SK-N-SH_RA	brain:	n/a	n/a
16	RAD21	chr4:159093665-159093997	GM12878	blood:	n/a	n/a
17	CTCF	chr4:159093313-159094293	HCT-116	colon:	n/a	n/a
18	CTCF	chr4:159093732-159093989	Kidney_OC	kidney:	n/a	n/a
19	CTCF	chr4:159093804-159093978	GM19238	blood:	n/a	n/a
20	POLR2A	chr4:159093650-159094097	IMR90	lung:	n/a	n/a
21	TAL1	chr4:159093821-159094069	K562	blood:	n/a	n/a
22	CTCF	chr4:159093610-159094008	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr4:159093650-159094029	GM12878	blood:	n/a	n/a
24	FOXA1	chr4:159093567-159094759	HepG2	liver:	n/a	n/a
25	RAD21	chr4:159093093-159094671	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr4:159093375-159094252	SK-N-SH	brain:	n/a	n/a
27	EP300	chr4:159093755-159094418	HepG2	liver:	n/a	n/a
28	MYBL2	chr4:159093259-159094511	HepG2	liver:	n/a	n/a
29	RAD21	chr4:159093630-159093985	A549	lung:	n/a	n/a
30	RAD21	chr4:159093436-159094080	HepG2	liver:	n/a	n/a
31	SMC3	chr4:159093685-159093989	K562	blood:	n/a	n/a
32	RAD21	chr4:159093561-159094055	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr4:159093558-159094045	A549	lung:	n/a	n/a
34	RAD21	chr4:159093717-159094001	HepG2	liver:	n/a	n/a
35	MBD4	chr4:159093455-159094388	HepG2	liver:	n/a	n/a
36	CTCF	chr4:159093592-159093992	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr4:159093617-159094120	MCF-7	breast:	n/a	n/a
38	RAD21	chr4:159093444-159093968	SK-N-SH_RA	brain:	n/a	n/a
39	RAD21	chr4:159093542-159094099	MCF-7	breast:	n/a	n/a
40	SMC3	chr4:159093216-159094265	SK-N-SH	brain:	n/a	n/a
41	SMC3	chr4:159093561-159094032	Hela-S3	cervix:	n/a	n/a
42	TBL1XR1	chr4:159093957-159094128	K562	blood:	n/a	n/a
43	RAD21	chr4:159093529-159094029	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr4:159093794-159093975	NHEK	skin:	n/a	n/a
45	POLR2A	chr4:159093911-159094405	HUVEC	blood vessel:	n/a	n/a
46	CTCF	chr4:159093527-159094142	IMR90	lung:	n/a	n/a
47	CTCF	chr4:159093820-159093970	GM12872	blood:	n/a	n/a
48	ARID3A	chr4:159093820-159094004	K562	blood:	n/a	n/a
49	EP300	chr4:159093549-159094525	HepG2	liver:	n/a	chr4:159093616-159093630
50	CTCF	chr4:159093736-159093961	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:159093915-159093965	ProgFib	skin:	n/a
2	chr4:159093915-159093965	Hepatocyte	liver:	n/a
3	chr4:159093915-159093965	IMR90	lung:	fetal
4	chr4:159093915-159093965	PFSK-1	brain:	n/a
5	chr4:159093915-159093965	AG04450	lung:	fetal
6	chr4:159093915-159093965	SK-N-MC	brain:	n/a
7	chr4:159093915-159093965	RPTEC	kidney:	n/a
8	chr4:159093915-159093965	AG09309	skin:	n/a
9	chr4:159093915-159093965	SKMC	muscle:	n/a
10	chr4:159093915-159093965	NT2-D1	testis:	n/a
11	chr4:159093915-159093965	BJ	skin:	n/a
12	chr4:159093915-159093965	NHBE	bronchial:	n/a
13	chr4:159093915-159093965	MCF-7	breast:	n/a
14	chr4:159093915-159093965	HCF	heart:	n/a
15	chr4:159093915-159093965	K562	blood:	n/a
16	chr4:159093915-159093965	HCT-116	colon:	n/a
17	chr4:159093915-159093965	Caco-2	colon:	n/a
18	chr4:159093915-159093965	T-47D	breast:	n/a
19	chr4:159093915-159093965	MCF10A-Er-Src	breast:	n/a
20	chr4:159093915-159093965	AG10803	skin:	n/a
21	chr4:159093915-159093965	NHDF-neo	bronchial:	n/a
22	chr4:159093915-159093965	HL-60	blood:	n/a
23	chr4:159093915-159093965	GM06990	blood:	n/a
24	chr4:159093915-159093965	NH-A	brain:	n/a
25	chr4:159093915-159093965	HEEpiC	esophagus:	n/a
26	chr4:159093915-159093965	PANC-1	pancreas:	n/a
27	chr4:159093915-159093965	HRE	kidney:	n/a
28	chr4:159093915-159093965	HepG2	liver:	n/a
29	chr4:159093915-159093965	AoSMC	blood vessel:	n/a
30	chr4:159093915-159093965	HCM	heart:	n/a
31	chr4:159093915-159093965	A549	lung:	n/a
32	chr4:159093915-159093965	HEK293	kidney:	embryo
33	chr4:159093915-159093965	SK-N-SH_RA	brain:	n/a
34	chr4:159093915-159093965	HRPEpiC	eye:	n/a
35	chr4:159093915-159093965	ECC-1	luminal epithelium:	n/a
36	chr4:159093915-159093965	PrEC	prostate:	n/a
37	chr4:159093915-159093965	GM19239	blood:	n/a
38	chr4:159093915-159093965	LNCaP	prostate:	n/a
39	chr4:159093915-159093965	Jurkat	blood:	n/a
40	chr4:159093915-159093965	NB4	blood:	n/a
41	chr4:159093915-159093965	GM12892	blood:	n/a
42	chr4:159093915-159093965	U87	brain:	n/a
43	chr4:159093915-159093965	HNPCEpiC	eye:	n/a
44	chr4:159093915-159093965	SK-N-SH	brain:	n/a
45	chr4:159093915-159093965	HCPEpiC	choroid plexus:	n/a
46	chr4:159093915-159093965	HUVEC	blood vessel:	n/a
47	chr4:159093915-159093965	BE2_C	brain:	n/a
48	chr4:159093915-159093965	AG04449	skin:	fetal
49	chr4:159093915-159093965	AG09319	gingival:	n/a
50	chr4:159093915-159093965	HPAEpiC	pulmonary alveolar:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM144-1	chr4:159093729-159094092	ENSG00000248429.1

No data

Variant related genes	Relation type
ENSG00000248429	TF binding region
FAM198B	TF binding region
FAM198B	CpG island
ENSG00000248429	CpG island

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10021199	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs10517685	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10517686	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11100152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11933839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11939690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11944517	0.80[ASW][hapmap]
rs17036992	0.90[EUR][1000 genomes]
rs17036995	0.90[EUR][1000 genomes]
rs17037201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17212066	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17212714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17271385	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17279270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881374	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4234916	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4508943	1.00[CHB][hapmap]
rs4510503	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6536290	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs6820988	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6834839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6837943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72691615	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691620	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691622	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691626	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691627	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691629	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691631	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691632	0.90[EUR][1000 genomes]
rs72691633	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691634	0.90[EUR][1000 genomes]
rs72691636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691649	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72695726	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72695736	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695741	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695744	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695745	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695747	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695748	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695749	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695750	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695751	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695753	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7678302	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9997618	0.90[CEU][hapmap];1.00[CHB][hapmap]

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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17037232	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs17037232	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs17037232	TMEM144	cis	Esophagus Muscularis	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159078600-159094000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:159085000-159095200	Active TSS	Aorta	Aorta
3	chr4:159085200-159094000	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr4:159085400-159095000	Active TSS	Right Atrium	heart
5	chr4:159085600-159095000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr4:159088400-159094400	Active TSS	Right Ventricle	heart
7	chr4:159088600-159094400	Active TSS	Fetal Heart	heart
8	chr4:159089000-159094600	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:159089200-159094200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:159089600-159094000	Active TSS	Colon Smooth Muscle	Colon
11	chr4:159089600-159094200	Active TSS	Colonic Mucosa	Colon
12	chr4:159089800-159094600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:159090000-159094000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:159090200-159094200	Active TSS	Left Ventricle	heart
15	chr4:159090200-159094200	Active TSS	Psoas Muscle	Psoas
16	chr4:159090200-159094200	Active TSS	HSMM	muscle
17	chr4:159090200-159094400	Active TSS	Fetal Intestine Large	intestine
18	chr4:159090200-159095000	Active TSS	HSMMtube	muscle
19	chr4:159090400-159094400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr4:159090800-159094000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:159090800-159094000	Active TSS	Brain Substantia Nigra	brain
22	chr4:159091000-159094000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:159091000-159094000	Active TSS	Fetal Kidney	kidney
24	chr4:159091000-159094000	Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:159091000-159094400	Active TSS	Fetal Intestine Small	intestine
26	chr4:159092400-159094000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:159092400-159094000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr4:159092400-159094400	Active TSS	HepG2	liver
29	chr4:159092600-159094000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:159092600-159094000	Active TSS	Duodenum Mucosa	Duodenum
31	chr4:159092600-159094200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:159092600-159094200	Active TSS	Fetal Muscle Trunk	muscle
33	chr4:159092600-159094200	Active TSS	Pancreas	Pancrea
34	chr4:159092600-159094200	Active TSS	Rectal Smooth Muscle	rectum
35	chr4:159092600-159094200	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr4:159092600-159094200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:159092600-159095200	Active TSS	Ovary	ovary
38	chr4:159092600-159095200	Weak transcription	Spleen	Spleen
39	chr4:159092600-159096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:159092600-159104000	Weak transcription	Lung	lung
41	chr4:159092800-159094000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr4:159092800-159094200	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr4:159092800-159097400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:159093000-159094000	Active TSS	Osteobl	bone
45	chr4:159093200-159094000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:159093200-159094200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:159093200-159094200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:159093200-159094200	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr4:159093200-159094600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr4:159093400-159094000	Enhancers	K562	blood

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