Variant report

Variant	rs4291501
Chromosome Location	chr1:151169157-151169158
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	SMC3	chr1:151168603-151169215	SK-N-SH	brain:	n/a	chr1:151168947-151168961
2	POLR2A	chr1:151169086-151169157	MCF-7	breast:	n/a	n/a
3	POLR2A	chr1:151168616-151169160	PANC-1	pancreas:	n/a	n/a
4	CTCF	chr1:151168589-151169250	MCF-7	breast:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
5	POLR2A	chr1:151166739-151169180	Hela-S3	cervix:	n/a	n/a
6	RAD21	chr1:151168717-151169177	HepG2	liver:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
7	POLR2A	chr1:151168591-151169198	Hela-S3	cervix:	n/a	n/a
8	ZNF384	chr1:151168156-151169230	GM12878	blood:	n/a	n/a
9	REST	chr1:151168635-151169170	A549	lung:	n/a	n/a
10	YY1	chr1:151168886-151169218	GM12892	blood:	n/a	n/a
11	CTCF	chr1:151168505-151169260	SK-N-SH	brain:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
12	RAD21	chr1:151168725-151169188	MCF-7	breast:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
13	NR2F2	chr1:151168664-151169212	K562	blood:	n/a	n/a
14	RAD21	chr1:151168593-151169284	HCT-116	colon:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
15	GATA3	chr1:151167330-151169342	MCF-7	breast:	n/a	n/a
16	MAZ	chr1:151168643-151169217	IMR90	lung:	n/a	n/a
17	POLR2A	chr1:151168684-151169166	PANC-1	pancreas:	n/a	n/a
18	SP1	chr1:151168658-151169212	A549	lung:	n/a	n/a
19	YY1	chr1:151168881-151169221	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:151168499-151169196	HepG2	liver:	n/a	n/a
21	RAD21	chr1:151168559-151169298	SK-N-SH	brain:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
22	CTCF	chr1:151168640-151169223	MCF-7	breast:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
23	RAD21	chr1:151168625-151169238	A549	lung:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
24	YY1	chr1:151169005-151169231	HepG2	liver:	n/a	n/a
25	CTCF	chr1:151168675-151169194	A549	lung:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
26	GATA2	chr1:151168719-151169181	HUVEC	blood vessel:	n/a	n/a
27	CTCF	chr1:151168517-151169191	HCT-116	colon:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
28	RAD21	chr1:151168649-151169253	MCF-7	breast:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
29	RAD21	chr1:151168656-151169199	ECC-1	luminal epithelium:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
30	GTF3C2	chr1:151166966-151169329	Hela-S3	cervix:	n/a	n/a
31	RAD21	chr1:151168727-151169165	A549	lung:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
32	GATA3	chr1:151168717-151169197	T-47D	breast:	n/a	n/a
33	BCLAF1	chr1:151168788-151169210	GM12878	blood:	n/a	n/a
34	TEAD4	chr1:151168760-151169169	K562	blood:	n/a	n/a
35	NFIC	chr1:151168674-151169188	HepG2	liver:	n/a	n/a
36	SP1	chr1:151168513-151169203	A549	lung:	n/a	n/a
37	TEAD4	chr1:151168652-151169188	HepG2	liver:	n/a	n/a
38	MAX	chr1:151168590-151169229	A549	lung:	n/a	n/a
39	CTCF	chr1:151167611-151169289	A549	lung:	n/a	chr1:151168948-151168961 chr1:151168947-151168968 chr1:151168948-151168956 chr1:151168945-151168963
40	YY1	chr1:151168781-151169188	HepG2	liver:	n/a	n/a
41	TCF12	chr1:151167702-151169247	SK-N-SH	brain:	n/a	chr1:151167924-151167932
42	ZNF384	chr1:151168760-151169212	K562	blood:	n/a	n/a
43	RAD21	chr1:151168636-151169231	HCT-116	colon:	n/a	chr1:151168951-151168963 chr1:151168946-151168965 chr1:151168949-151168962 chr1:151168951-151168961
44	GATA3	chr1:151168565-151169254	MCF-7	breast:	n/a	n/a
45	YY1	chr1:151168859-151169257	GM12878	blood:	n/a	n/a
46	HA-E2F1	chr1:151168782-151169221	MCF-7	breast:	n/a	n/a
47	POLR2A	chr1:151168918-151169173	HepG2	liver:	n/a	n/a
48	POU2F2	chr1:151168721-151169196	GM12878	blood:	n/a	n/a
49	MYBL2	chr1:151168582-151169221	HepG2	liver:	n/a	n/a
50	GATA3	chr1:151168713-151169159	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
2	chr1:151167814..151170369-chr1:151245194..151246986,2	MCF-7	breast:
3	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
4	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
5	chr1:151136716..151140911-chr1:151168778..151172657,5	MCF-7	breast:
6	chr1:151168523..151169395-chr1:151224075..151225052,3	K562	blood:
7	chr1:151168724..151174586-chr1:151252405..151256834,10	MCF-7	breast:
8	chr1:151166438..151169666-chr1:151298490..151301352,3	MCF-7	breast:
9	chr1:151136857..151140256-chr1:151168802..151172321,4	MCF-7	breast:
10	chr1:151168437..151169434-chr1:151223818..151224818,4	MCF-7	breast:
11	chr1:151041779..151043840-chr1:151166772..151169795,3	MCF-7	breast:
12	chr1:151167452..151169662-chr1:151226503..151228827,3	MCF-7	breast:

Variant related genes	Relation type
VPS72	TF binding region
PIP5K1A	TF binding region
ENSG00000273481	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000163156	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10749660	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888406	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888408	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11204785	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204791	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11807075	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12022732	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12040384	0.82[ASN][1000 genomes]
rs12048670	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12062719	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12080778	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12407426	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16827941	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16833079	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892196	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275900	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs41302131	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4520422	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970944	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971013	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971015	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971016	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971021	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971023	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971025	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971026	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58323986	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61817972	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587559	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587562	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681071	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681163	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6683396	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686402	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6695344	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6701325	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7521064	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527032	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532935	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7539584	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7544947	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151162800-151170200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:151162800-151170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151163000-151170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151163200-151170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:151163200-151170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:151163200-151170400	Weak transcription	Gastric	stomach
7	chr1:151163200-151170400	Weak transcription	Left Ventricle	heart
8	chr1:151163400-151170000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:151163400-151170200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:151163400-151170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:151163400-151170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:151163400-151170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:151163400-151170200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:151163400-151170400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:151163600-151170200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:151163600-151170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:151163600-151170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:151166400-151169200	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr1:151166600-151169200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:151166800-151170200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:151167000-151169200	Active TSS	Duodenum Mucosa	Duodenum
22	chr1:151167000-151169600	Active TSS	Placenta	Placenta
23	chr1:151167000-151172000	Active TSS	Colonic Mucosa	Colon
24	chr1:151167200-151169800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:151167400-151169200	Active TSS	A549	lung
26	chr1:151167400-151169600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:151167600-151169600	Weak transcription	Esophagus	oesophagus
28	chr1:151167800-151170200	Enhancers	Fetal Intestine Small	intestine
29	chr1:151168000-151169200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:151168000-151169200	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr1:151168000-151170200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:151168000-151170200	Active TSS	HepG2	liver
33	chr1:151168000-151170400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:151168000-151170400	Weak transcription	Pancreas	Pancrea
35	chr1:151168000-151170800	Weak transcription	Lung	lung
36	chr1:151168200-151169200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:151168200-151170200	Weak transcription	HSMMtube	muscle
38	chr1:151168200-151170200	Weak transcription	NHLF	lung
39	chr1:151168200-151170400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr1:151168400-151169200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:151168600-151169200	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr1:151168600-151169200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:151168600-151169200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr1:151168600-151169200	Enhancers	Colon Smooth Muscle	Colon
45	chr1:151168600-151169200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:151168600-151169200	Active TSS	Psoas Muscle	Psoas
47	chr1:151168600-151169400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr1:151168600-151169400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:151168600-151169400	Enhancers	Dnd41	blood
50	chr1:151168600-151170600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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