Variant report

Variant	rs74127407
Chromosome Location	chr1:150045224-150045225
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	CTCF	chr1:150045160-150045310	HCFaa	heart:	n/a	chr1:150045229-150045250
2	CTCF	chr1:150045120-150045270	AG09309	skin:	n/a	chr1:150045229-150045250
3	CTCF	chr1:150045160-150045310	HA-sp	spinal cord:	n/a	chr1:150045229-150045250
4	CTCF	chr1:150045140-150045290	AG09319	gingival:	n/a	chr1:150045229-150045250
5	CTCF	chr1:150045160-150045310	HPF	lung:	n/a	chr1:150045229-150045250
6	CTCF	chr1:150045120-150045270	SK-N-SH_RA	brain:	n/a	chr1:150045229-150045250
7	RAD21	chr1:150044996-150045519	IMR90	lung:	n/a	n/a
8	CTCF	chr1:150045120-150045270	GM12873	blood:	n/a	chr1:150045229-150045250
9	CTCF	chr1:150045120-150045270	HUVEC	blood vessel:	n/a	chr1:150045229-150045250
10	CTCF	chr1:150045132-150045314	K562	blood:	n/a	chr1:150045229-150045250
11	RAD21	chr1:150045178-150045362	K562	blood:	n/a	n/a
12	RAD21	chr1:150044762-150045628	SK-N-SH	brain:	n/a	n/a
13	CTCF	chr1:150045120-150045270	AG04449	skin:	n/a	chr1:150045229-150045250
14	CTCF	chr1:150045160-150045310	GM12874	blood:	n/a	chr1:150045229-150045250
15	CTCF	chr1:150045140-150045290	GM12878	blood:	n/a	chr1:150045229-150045250
16	RAD21	chr1:150044922-150045449	HCT-116	colon:	n/a	n/a
17	CTCF	chr1:150045120-150045270	MCF-7	breast:	n/a	chr1:150045229-150045250
18	CTCF	chr1:150045086-150045376	HUVEC	blood vessel:	n/a	chr1:150045229-150045250
19	CTCF	chr1:150045160-150045310	NHDF-neo	bronchial:	n/a	chr1:150045229-150045250
20	CTCF	chr1:150045180-150045330	GM12873	blood:	n/a	chr1:150045229-150045250
21	RAD21	chr1:150045076-150045430	GM12878	blood:	n/a	n/a
22	RAD21	chr1:150045045-150045542	A549	lung:	n/a	n/a
23	CTCF	chr1:150045126-150045363	Lung_OC	lung:	n/a	chr1:150045229-150045250
24	RAD21	chr1:150044954-150045535	A549	lung:	n/a	n/a
25	CTCF	chr1:150045123-150045310	GM10266	blood:	n/a	chr1:150045229-150045250
26	CTCF	chr1:150045086-150045355	Spleen_OC	spleen:	n/a	chr1:150045229-150045250
27	CTCF	chr1:150045140-150045290	K562	blood:	n/a	chr1:150045229-150045250
28	CTCF	chr1:150045031-150045424	GM12878	blood:	n/a	chr1:150045229-150045250
29	CTCF	chr1:150045140-150045290	HMF	breast:	n/a	chr1:150045229-150045250
30	CTCF	chr1:150045160-150045310	AG10803	skin:	n/a	chr1:150045229-150045250
31	CTCF	chr1:150045170-150045306	Pancreas_OC	pancreas:	n/a	chr1:150045229-150045250
32	CTCF	chr1:150045100-150045250	SAEC	small airway:	n/a	chr1:150045229-150045250
33	RAD21	chr1:150044954-150045457	MCF-7	breast:	n/a	n/a
34	CTCF	chr1:150045120-150045270	HL-60	blood:	n/a	chr1:150045229-150045250
35	CTCF	chr1:150045080-150045230	HRE	kidney:	n/a	n/a
36	CTCF	chr1:150045145-150045342	LNCaP	prostate:	n/a	chr1:150045229-150045250
37	CTCF	chr1:150045160-150045310	HPAF	blood vessel:	n/a	chr1:150045229-150045250
38	CTCF	chr1:150045160-150045310	HMF	breast:	n/a	chr1:150045229-150045250
39	CTCF	chr1:150045100-150045250	HCM	heart:	n/a	chr1:150045229-150045250
40	CTCF	chr1:150045120-150045270	GM12865	blood:	n/a	chr1:150045229-150045250
41	CTCF	chr1:150045039-150045462	IMR90	lung:	n/a	chr1:150045229-150045250
42	CTCF	chr1:150044969-150045526	MCF-7	breast:	n/a	chr1:150045229-150045250
43	CTCF	chr1:150045120-150045270	GM12866	blood:	n/a	chr1:150045229-150045250
44	CTCF	chr1:150045120-150045270	HPF	lung:	n/a	chr1:150045229-150045250
45	CTCF	chr1:150045180-150045330	GM12870	blood:	n/a	chr1:150045229-150045250
46	CTCF	chr1:150045120-150045270	WERI-Rb-1	eye:	n/a	chr1:150045229-150045250
47	CTCF	chr1:150045120-150045270	GM12864	blood:	n/a	chr1:150045229-150045250
48	CTCF	chr1:150044918-150045490	HCT-116	colon:	n/a	chr1:150045229-150045250
49	CTCF	chr1:150045000-150045270	BE2_C	brain:	n/a	chr1:150045229-150045250
50	CTCF	chr1:150045140-150045290	NHLF	lung:	n/a	chr1:150045229-150045250

No.	Distal block	Cell Line	Cell type
1	chr1:150035483..150047454-chr1:150129931..150138567,28	MCF-7	breast:
2	chr1:149898320..149901197-chr1:150045143..150046791,2	MCF-7	breast:
3	chr1:150044821..150045736-chr1:150140877..150141818,5	K562	blood:
4	chr1:150044965..150047387-chr1:150136766..150139842,3	MCF-7	breast:
5	chr1:150045133..150046720-chr1:150047065..150048856,2	MCF-7	breast:
6	chr1:150045026..150046248-chr1:150134083..150135043,5	MCF-7	breast:
7	chr1:150032474..150034283-chr1:150044859..150046740,2	K562	blood:
8	chr1:150044299..150047300-chr1:150141169..150143269,3	MCF-7	breast:
9	chr1:150043719..150046734-chr1:150113127..150116158,3	MCF-7	breast:
10	chr1:149858840..149861713-chr1:150044592..150047147,2	MCF-7	breast:
11	chr1:150045161..150045935-chr1:150137894..150138811,3	MCF-7	breast:
12	chr1:150040162..150042986-chr1:150044967..150046584,2	K562	blood:
13	chr1:150044800..150045776-chr1:150140744..150141829,14	MCF-7	breast:
14	chr1:149982418..149984722-chr1:150044513..150046675,2	K562	blood:
15	chr1:150043953..150046600-chr1:150048139..150050720,2	K562	blood:
16	chr1:150044759..150045629-chr1:150122066..150122882,2	MCF-7	breast:
17	chr1:150043397..150045227-chr1:150050265..150052800,2	MCF-7	breast:
18	chr1:150044647..150045690-chr1:150137879..150138875,5	K562	blood:
19	chr1:150045014..150045693-chr1:150140910..150141616,3	MCF-7	breast:

Variant related genes	Relation type
VPS45	TF binding region
ENSG00000143368	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000136631	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs55643510	0.92[AFR][1000 genomes]
rs55989593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58106888	0.92[AFR][1000 genomes]
rs60124736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60138147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62622370	0.92[AFR][1000 genomes]
rs72692896	0.91[AFR][1000 genomes]
rs74124301	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127405	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74127416	0.92[AFR][1000 genomes]
rs74127419	0.92[AFR][1000 genomes]
rs74127421	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases
2	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150040000-150050200	Weak transcription	Spleen	Spleen
2	chr1:150040200-150046000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:150040200-150090800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:150040400-150046000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:150040400-150046200	Weak transcription	Fetal Thymus	thymus
6	chr1:150040400-150047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:150040400-150047800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr1:150040400-150047800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:150040400-150049800	Weak transcription	Ovary	ovary
10	chr1:150040400-150049800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:150040400-150050000	Weak transcription	Lung	lung
12	chr1:150040400-150056400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:150040400-150061600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:150040400-150078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:150040400-150082800	Weak transcription	Small Intestine	intestine
16	chr1:150040400-150086800	Weak transcription	Esophagus	oesophagus
17	chr1:150040400-150121400	Weak transcription	Pancreas	Pancrea
18	chr1:150040600-150046200	Weak transcription	Colonic Mucosa	Colon
19	chr1:150040600-150048200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:150040600-150072200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:150040600-150092000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:150040800-150045600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:150040800-150046000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:150040800-150048400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:150040800-150048800	Weak transcription	Primary B cells from cord blood	blood
26	chr1:150040800-150049000	Weak transcription	Primary T cells from cord blood	blood
27	chr1:150040800-150049800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr1:150040800-150049800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:150040800-150049800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:150040800-150054400	Weak transcription	Aorta	Aorta
31	chr1:150041000-150047400	Strong transcription	Placenta	Placenta
32	chr1:150041000-150047600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:150041000-150048200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr1:150041000-150048200	Weak transcription	Fetal Brain Female	brain
35	chr1:150041000-150048800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:150041000-150049200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr1:150041000-150049800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:150041000-150049800	Weak transcription	Thymus	Thymus
39	chr1:150041000-150049800	Weak transcription	HSMMtube	muscle
40	chr1:150041000-150053600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:150041000-150064000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr1:150041000-150114400	Weak transcription	Right Ventricle	heart
43	chr1:150041200-150045800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:150041200-150045800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr1:150041200-150046600	Weak transcription	Fetal Intestine Large	intestine
46	chr1:150041200-150048800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:150041200-150049200	Weak transcription	HepG2	liver
48	chr1:150041200-150049800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr1:150041200-150054800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:150041400-150045600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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