Variant report

Variant	rs10888438
Chromosome Location	chr1:151809342-151809343
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	TCF7L2	chr1:151809018-151809922	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:151809002-151809604	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr1:151808951-151809515	MCF10A-Er-Src	breast:	n/a	chr1:151809446-151809454 chr1:151809402-151809414
4	NR2F2	chr1:151808672-151810171	MCF-7	breast:	n/a	n/a
5	RAD21	chr1:151808665-151809426	A549	lung:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
6	TCF12	chr1:151809011-151809776	ECC-1	luminal epithelium:	n/a	chr1:151809368-151809375 chr1:151809105-151809112
7	CTCF	chr1:151808347-151809619	SK-N-SH	brain:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107 chr1:151809598-151809611
8	ZKSCAN1	chr1:151808901-151809458	Hela-S3	cervix:	n/a	n/a
9	MAX	chr1:151808870-151809747	Hela-S3	cervix:	n/a	n/a
10	GATA3	chr1:151808902-151809829	T-47D	breast:	n/a	chr1:151809442-151809452
11	RAD21	chr1:151808311-151809428	SK-N-SH	brain:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
12	TFAP2A	chr1:151808935-151809637	Hela-S3	cervix:	n/a	chr1:151809125-151809140 chr1:151809126-151809137
13	RAD21	chr1:151808777-151809393	ECC-1	luminal epithelium:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
14	NFIC	chr1:151808690-151809959	ECC-1	luminal epithelium:	n/a	n/a
15	SMC3	chr1:151808827-151809864	Hela-S3	cervix:	n/a	chr1:151809488-151809498 chr1:151809091-151809105
16	CTCF	chr1:151808575-151809469	HCT-116	colon:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107
17	CTCF	chr1:151808336-151809433	A549	lung:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107
18	TFAP2C	chr1:151808963-151809606	Hela-S3	cervix:	n/a	chr1:151809125-151809140
19	SPI1	chr1:151809342-151809505	K562	blood:	n/a	chr1:151809443-151809456
20	ELK1	chr1:151809085-151809526	Hela-S3	cervix:	n/a	n/a
21	SPI1	chr1:151808816-151809601	HL-60	blood:	n/a	chr1:151809443-151809456 chr1:151809163-151809176
22	TCF12	chr1:151808790-151809395	A549	lung:	n/a	chr1:151808820-151808827 chr1:151809368-151809375 chr1:151809105-151809112
23	RCOR1	chr1:151808943-151809880	Hela-S3	cervix:	n/a	n/a
24	SMC3	chr1:151808258-151809706	SK-N-SH	brain:	n/a	chr1:151809488-151809498 chr1:151809091-151809105
25	CEBPB	chr1:151808927-151809346	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:151809325-151809471	MCF-7	breast:	n/a	n/a
27	ZNF143	chr1:151808903-151809484	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr1:151809260-151809410	GM12873	blood:	n/a	n/a
29	MAZ	chr1:151808963-151809857	Hela-S3	cervix:	n/a	n/a
30	BRCA1	chr1:151808884-151809800	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr1:151809240-151809390	HA-sp	spinal cord:	n/a	n/a
32	CTCF	chr1:151809320-151809470	WERI-Rb-1	eye:	n/a	n/a
33	RAD21	chr1:151808714-151809824	MCF-7	breast:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104 chr1:151809598-151809612
34	GTF2F1	chr1:151808950-151809618	Hela-S3	cervix:	n/a	n/a
35	JUN	chr1:151809034-151809343	H1-hESC	embryonic stem cell:	n/a	n/a
36	MXI1	chr1:151808967-151809714	Hela-S3	cervix:	n/a	n/a
37	RUNX3	chr1:151808848-151809444	GM12878	blood:	n/a	chr1:151809314-151809331
38	RAD21	chr1:151808822-151809829	Hela-S3	cervix:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151809087-151809106 chr1:151809090-151809104 chr1:151809598-151809612
39	RFX5	chr1:151808931-151809631	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr1:151808306-151809793	MCF-7	breast:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107 chr1:151809598-151809611
41	RAD21	chr1:151808602-151809609	HCT-116	colon:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
42	CTCF	chr1:151808773-151809427	MCF-7	breast:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107
43	MAX	chr1:151808908-151809612	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr1:151808718-151809412	ECC-1	luminal epithelium:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
45	POLR2A	chr1:151809053-151809507	HepG2	liver:	n/a	n/a
46	CTCF	chr1:151808782-151809375	HCT-116	colon:	n/a	chr1:151808816-151808829 chr1:151809084-151809105 chr1:151809091-151809104 chr1:151809095-151809104 chr1:151809089-151809107
47	CHD2	chr1:151809015-151809788	Hela-S3	cervix:	n/a	chr1:151809583-151809593 chr1:151809668-151809678
48	ZNF217	chr1:151808979-151809749	MCF-7	breast:	n/a	n/a
49	RAD21	chr1:151808601-151809579	HCT-116	colon:	n/a	chr1:151809360-151809373 chr1:151809096-151809105 chr1:151808819-151808831 chr1:151809087-151809106 chr1:151809090-151809104
50	FOXA1	chr1:151809328-151809724	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151510584..151515702-chr1:151808389..151812312,7	MCF-7	breast:
2	chr1:151735784..151737318-chr1:151808411..151810675,2	MCF-7	breast:
3	chr1:151712042..151713073-chr1:151808628..151809658,5	MCF-7	breast:
4	chr1:151483121..151485992-chr1:151808020..151810121,3	MCF-7	breast:
5	chr1:151707202..151708163-chr1:151808657..151809536,5	MCF-7	breast:
6	chr1:151804539..151806807-chr1:151808292..151812161,4	K562	blood:
7	chr1:151665450..151666493-chr1:151808600..151809515,6	K562	blood:
8	chr1:19410890..19413871-chr1:151808457..151811077,2	MCF-7	breast:
9	chr1:151808928..151809951-chr1:151853655..151854418,3	MCF-7	breast:
10	chr1:151808355..151810594-chr1:151852540..151855427,2	MCF-7	breast:
11	chr1:151535409..151537724-chr1:151807504..151809415,2	MCF-7	breast:
12	chr1:151712112..151713087-chr1:151808881..151809397,2	MCF-7	breast:
13	chr1:151809106..151809860-chr3:64016088..64016677,2	MCF-7	breast:
14	chr1:151809121..151809703-chr4:128801479..128802412,2	Hela-S3	cervix:
15	chr1:151808934..151809634-chr1:151853928..151854568,2	MCF-7	breast:
16	chr1:151717253..151722089-chr1:151808382..151812448,4	MCF-7	breast:
17	chr1:151566525..151567546-chr1:151808737..151809625,3	MCF-7	breast:
18	chr1:151566301..151567308-chr1:151808522..151809558,4	K562	blood:
19	chr1:151808068..151810311-chr1:151964159..151966593,4	MCF-7	breast:
20	chr1:151430044..151432386-chr1:151809146..151811411,2	MCF-7	breast:
21	chr1:151795525..151798477-chr1:151809091..151811611,2	MCF-7	breast:
22	chr1:151707320..151708173-chr1:151808673..151809435,3	MCF-7	breast:
23	chr1:151807915..151809581-chr1:151880993..151883384,2	MCF-7	breast:
24	chr1:151678020..151678605-chr1:151808685..151809547,3	MCF-7	breast:
25	chr1:151506889..151507829-chr1:151808656..151809532,4	K562	blood:
26	chr1:151507235..151508171-chr1:151808641..151809567,3	MCF-7	breast:
27	chr1:151737845..151739446-chr1:151807835..151809474,2	MCF-7	breast:
28	chr1:151416014..151416766-chr1:151808595..151809606,5	K562	blood:

Variant related genes	Relation type
RORC	TF binding region
ENSG00000143450	Chromatin interaction
ENSG00000142731	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000232937	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000206980	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10788810	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029913	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12122596	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12140021	0.87[ASN][1000 genomes]
rs2130529	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6587622	0.83[EUR][1000 genomes]
rs6667460	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551686	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7551806	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151802000-151809400	Enhancers	Fetal Thymus	thymus
2	chr1:151802400-151810400	Weak transcription	Right Atrium	heart
3	chr1:151802800-151811000	Enhancers	Placenta	Placenta
4	chr1:151804400-151810200	Weak transcription	Gastric	stomach
5	chr1:151804400-151810600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:151804600-151812000	Enhancers	Pancreas	Pancrea
7	chr1:151804800-151809400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:151805000-151810200	Weak transcription	Right Ventricle	heart
9	chr1:151805200-151810400	Weak transcription	Lung	lung
10	chr1:151805200-151810600	Enhancers	Dnd41	blood
11	chr1:151805400-151809400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:151805400-151810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:151805600-151809800	Enhancers	Duodenum Mucosa	Duodenum
14	chr1:151805600-151811200	Weak transcription	Brain Angular Gyrus	brain
15	chr1:151805800-151809600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr1:151806000-151810400	Weak transcription	Esophagus	oesophagus
17	chr1:151806200-151810400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:151806200-151811000	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:151806400-151811800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:151806600-151809400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:151806600-151809400	Weak transcription	Stomach Mucosa	stomach
22	chr1:151806800-151809400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:151806800-151810000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:151807000-151809400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr1:151807000-151809400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:151807000-151810800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:151807200-151809600	Enhancers	HepG2	liver
28	chr1:151807200-151810600	Enhancers	Liver	Liver
29	chr1:151808200-151810400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:151808400-151809600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:151808400-151809600	Enhancers	Fetal Intestine Large	intestine
32	chr1:151808400-151810000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:151808400-151810400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:151808400-151810400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
35	chr1:151808400-151810800	Enhancers	HMEC	breast
36	chr1:151808600-151809600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:151808600-151809600	Enhancers	Fetal Intestine Small	intestine
38	chr1:151808600-151809800	Enhancers	Primary hematopoietic stem cells	blood
39	chr1:151808600-151810400	Enhancers	NHEK	skin
40	chr1:151808800-151809400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:151808800-151809400	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:151808800-151809400	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr1:151808800-151809600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:151808800-151809800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr1:151808800-151810000	Enhancers	A549	lung
46	chr1:151808800-151810200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:151808800-151810200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr1:151808800-151810400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:151808800-151810400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:151808800-151810800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links