Variant report

Variant	rs1447093
Chromosome Location	chr4:106553364-106553365
allele	C/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	chr4:106553320-106553470	AG10803	skin:	n/a	chr4:106553357-106553375
2	CTCF	chr4:106553360-106553510	NHEK	skin:	n/a	n/a
3	CTCF	chr4:106553320-106553470	GM06990	blood:	n/a	chr4:106553357-106553375
4	CTCF	chr4:106553284-106553408	HepG2	liver:	n/a	chr4:106553357-106553375
5	CTCF	chr4:106553280-106553430	AG09319	gingival:	n/a	chr4:106553357-106553375
6	CTCF	chr4:106553320-106553470	AoAF	blood vessel:	n/a	chr4:106553357-106553375
7	CTCF	chr4:106553300-106553450	HRPEpiC	eye:	n/a	chr4:106553357-106553375
8	CTCF	chr4:106553240-106553510	HA-sp	spinal cord:	n/a	chr4:106553357-106553375
9	CTCF	chr4:106553359-106553443	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr4:106553320-106553470	HRPEpiC	eye:	n/a	chr4:106553357-106553375
11	CTCF	chr4:106553293-106553504	Lung_OC	lung:	n/a	chr4:106553357-106553375
12	CTCF	chr4:106553322-106553478	LNCaP	prostate:	n/a	chr4:106553357-106553375
13	CTCF	chr4:106553280-106553430	HRE	kidney:	n/a	chr4:106553357-106553375
14	CTCF	chr4:106553280-106553430	BE2_C	brain:	n/a	chr4:106553357-106553375
15	CTCF	chr4:106553280-106553430	GM06990	blood:	n/a	chr4:106553357-106553375
16	CTCF	chr4:106553300-106553450	HRE	kidney:	n/a	chr4:106553357-106553375
17	CTCF	chr4:106553300-106553450	HA-sp	spinal cord:	n/a	chr4:106553357-106553375
18	CTCF	chr4:106553280-106553430	NHLF	lung:	n/a	chr4:106553357-106553375
19	CTCF	chr4:106553280-106553430	HL-60	blood:	n/a	chr4:106553357-106553375
20	CTCF	chr4:106553267-106553486	Kidney_OC	kidney:	n/a	chr4:106553357-106553375
21	CTCF	chr4:106553340-106553490	AG09309	skin:	n/a	chr4:106553357-106553375
22	CTCF	chr4:106553280-106553430	HFF	foreskin:	n/a	chr4:106553357-106553375
23	CTCF	chr4:106553320-106553470	GM12875	blood:	n/a	chr4:106553357-106553375
24	CTCF	chr4:106553300-106553450	AG09319	gingival:	n/a	chr4:106553357-106553375
25	CTCF	chr4:106553260-106553410	HFF-Myc	foreskin:	n/a	chr4:106553357-106553375
26	CTCF	chr4:106553340-106553490	BE2_C	brain:	n/a	chr4:106553357-106553375
27	CTCF	chr4:106553300-106553450	AoAF	blood vessel:	n/a	chr4:106553357-106553375
28	RAD21	chr4:106553165-106553452	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr4:106553280-106553430	AG10803	skin:	n/a	chr4:106553357-106553375
30	CTCF	chr4:106553278-106553450	Medullo	brain:	n/a	chr4:106553357-106553375
31	CTCF	chr4:106553280-106553430	HEEpiC	esophagus:	n/a	chr4:106553357-106553375
32	CTCF	chr4:106553220-106553370	AG09309	skin:	n/a	n/a
33	CTCF	chr4:106553260-106553410	HMF	breast:	n/a	chr4:106553357-106553375
34	CTCF	chr4:106553320-106553470	HMF	breast:	n/a	chr4:106553357-106553375
35	CTCF	chr4:106553285-106553512	Spleen_OC	spleen:	n/a	chr4:106553357-106553375

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106507986..106508713-chr4:106552891..106553776,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF38	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10017111	1.00[CHB][hapmap]
rs10023798	0.85[CEU][hapmap]
rs10025790	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032142	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032283	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034172	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097895	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726715	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138544	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13147012	0.83[EUR][1000 genomes]
rs1447094	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1447098	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447099	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447100	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447101	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036041	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036049	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036098	0.85[CEU][hapmap]
rs2044536	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2121558	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2193856	0.83[CEU][hapmap]
rs2216515	0.83[CEU][hapmap]
rs2544402	0.83[CEU][hapmap]
rs2553446	0.83[CEU][hapmap]
rs2553456	0.83[CEU][hapmap]
rs2553460	0.83[CEU][hapmap]
rs2553461	0.83[CEU][hapmap]
rs2553463	0.83[CEU][hapmap]
rs28415919	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796920	0.85[CEU][hapmap]
rs3822277	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4484305	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67822595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833345	0.91[CEU][hapmap]
rs7680134	0.84[EUR][1000 genomes]
rs7686722	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699846	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921113	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9999133	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999326	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106525400-106558600	Weak transcription	Fetal Intestine Large	intestine
2	chr4:106527200-106559000	Weak transcription	Fetal Intestine Small	intestine
3	chr4:106540600-106553800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:106545200-106577800	Weak transcription	Pancreas	Pancrea
5	chr4:106545800-106558600	Weak transcription	Left Ventricle	heart
6	chr4:106546000-106553800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:106546000-106555800	Weak transcription	Fetal Lung	lung
8	chr4:106546000-106558200	Weak transcription	Brain Substantia Nigra	brain
9	chr4:106546200-106554000	Weak transcription	Small Intestine	intestine
10	chr4:106547000-106553800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:106549400-106555200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:106549600-106555600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:106549600-106558600	Weak transcription	Gastric	stomach
14	chr4:106549800-106553400	Weak transcription	Stomach Mucosa	stomach
15	chr4:106550600-106559400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:106551600-106555200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:106551800-106554000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:106551800-106554800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:106551800-106555400	Enhancers	HMEC	breast
20	chr4:106552400-106555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:106552400-106555600	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:106552400-106555600	Enhancers	GM12878-XiMat	blood
23	chr4:106552400-106558400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:106552600-106554200	Weak transcription	Fetal Heart	heart
25	chr4:106552600-106555000	Weak transcription	Fetal Brain Male	brain
26	chr4:106552800-106554400	Weak transcription	Colon Smooth Muscle	Colon
27	chr4:106552800-106555600	Weak transcription	Brain Anterior Caudate	brain
28	chr4:106552800-106558200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr4:106552800-106558400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:106552800-106558400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:106553000-106553400	Flanking Active TSS	NHEK	skin
32	chr4:106553000-106553600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr4:106553200-106554000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr4:106553200-106559000	Weak transcription	Fetal Kidney	kidney

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