Variant report

Variant	rs72935816
Chromosome Location	chr3:101405313-101405314
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	USF2	chr3:101404818-101405833	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr3:101405307-101405671	GM12891	blood:	n/a	n/a
3	SP1	chr3:101405242-101405851	GM12878	blood:	n/a	n/a
4	CUX1	chr3:101405184-101405819	GM12878	blood:	n/a	n/a
5	CTCF	chr3:101405277-101405504	GM19239	blood:	n/a	n/a
6	YY1	chr3:101404956-101405870	GM12878	blood:	n/a	n/a
7	SPI1	chr3:101405275-101405969	GM12878	blood:	n/a	chr3:101405706-101405713
8	IRF4	chr3:101405174-101405895	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:101404294-101405983	H1-hESC	embryonic stem cell:	n/a	n/a
10	SRF	chr3:101404908-101405885	MCF-7	breast:	n/a	chr3:101405578-101405592 chr3:101405582-101405593 chr3:101405579-101405594 chr3:101405578-101405595 chr3:101405580-101405591 chr3:101405581-101405592 chr3:101405576-101405594 chr3:101405582-101405591
11	PML	chr3:101405282-101405868	GM12878	blood:	n/a	n/a
12	TAF1	chr3:101404766-101405966	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr3:101405252-101405891	A549	lung:	n/a	n/a
14	SMC3	chr3:101405007-101405797	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:101404511-101405974	SK-N-SH	brain:	n/a	n/a
16	CTCF	chr3:101405280-101405430	HPF	lung:	n/a	n/a
17	MXI1	chr3:101404314-101405916	SK-N-SH	brain:	n/a	n/a
18	MYC	chr3:101405072-101406012	K562	blood:	n/a	chr3:101405791-101405800
19	MAX	chr3:101404876-101405946	NB4	blood:	n/a	chr3:101405791-101405800
20	TAF1	chr3:101405266-101405833	SK-N-SH	brain:	n/a	n/a
21	SP4	chr3:101405258-101405767	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZBTB33	chr3:101405225-101405966	HCT-116	colon:	n/a	n/a
23	POLR2A	chr3:101402873-101406294	GM12878	blood:	n/a	n/a
24	CTCF	chr3:101405264-101405732	Spleen_OC	spleen:	n/a	n/a
25	SRF	chr3:101405146-101405905	MCF-7	breast:	n/a	chr3:101405578-101405592 chr3:101405582-101405593 chr3:101405579-101405594 chr3:101405578-101405595 chr3:101405580-101405591 chr3:101405581-101405592 chr3:101405576-101405594 chr3:101405582-101405591
26	BCLAF1	chr3:101404834-101405898	GM12878	blood:	n/a	chr3:101405790-101405799 chr3:101405791-101405800
27	MBD4	chr3:101405113-101405854	HepG2	liver:	n/a	n/a
28	IRF3	chr3:101405250-101405650	GM12878	blood:	n/a	n/a
29	TAF1	chr3:101405155-101405867	GM12892	blood:	n/a	n/a
30	CTCF	chr3:101405180-101405330	RPTEC	kidney:	n/a	n/a
31	SIN3AK20	chr3:101405049-101405859	PANC-1	pancreas:	n/a	n/a
32	JUN	chr3:101405158-101405921	K562	blood:	n/a	chr3:101405791-101405799 chr3:101405790-101405799 chr3:101405653-101405666 chr3:101405791-101405800 chr3:101405792-101405799 chr3:101405789-101405801
33	JUND	chr3:101405278-101406281	GM12878	blood:	n/a	chr3:101405791-101405799 chr3:101405790-101405799 chr3:101405791-101405800 chr3:101405792-101405799 chr3:101405789-101405801
34	ZBTB33	chr3:101405309-101405847	HepG2	liver:	n/a	n/a
35	RELA	chr3:101404847-101405871	GM10847	blood:	n/a	n/a
36	POLR2A	chr3:101405236-101405876	GM10847	blood:	n/a	n/a
37	POLR2A	chr3:101404534-101405897	PANC-1	pancreas:	n/a	n/a
38	MAX	chr3:101405083-101405884	ECC-1	luminal epithelium:	n/a	chr3:101405791-101405800
39	SRF	chr3:101405213-101405827	ECC-1	luminal epithelium:	n/a	chr3:101405578-101405592 chr3:101405582-101405593 chr3:101405579-101405594 chr3:101405578-101405595 chr3:101405580-101405591 chr3:101405581-101405592 chr3:101405576-101405594 chr3:101405582-101405591
40	YY1	chr3:101405073-101405892	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:101404930-101406029	HUVEC	blood vessel:	n/a	n/a
42	JUND	chr3:101405284-101405949	HepG2	liver:	n/a	chr3:101405791-101405799 chr3:101405790-101405799 chr3:101405791-101405800 chr3:101405792-101405799 chr3:101405789-101405801
43	CTCF	chr3:101405200-101405350	HCM	heart:	n/a	n/a
44	CTCF	chr3:101405260-101405410	HPF	lung:	n/a	n/a
45	YY1	chr3:101405187-101405710	GM12892	blood:	n/a	n/a
46	CREB1	chr3:101405076-101405901	HepG2	liver:	n/a	chr3:101405655-101405668
47	CEBPB	chr3:101405159-101405940	HepG2	liver:	n/a	n/a
48	MAZ	chr3:101404911-101406067	IMR90	lung:	n/a	chr3:101405791-101405800
49	MAX	chr3:101405184-101405882	K562	blood:	n/a	chr3:101405791-101405800
50	POLR2A	chr3:101405238-101405814	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:159894811..159895698-chr3:101405185..101405704,2	Hela-S3	cervix:
2	chr3:101405192..101407713-chr3:101497187..101499121,2	MCF-7	breast:
3	chr3:101405090..101405836-chr9:127702816..127703490,2	Hela-S3	cervix:
4	chr3:39448010..39448706-chr3:101404983..101405656,2	Hela-S3	cervix:
5	chr3:101405211..101405953-chr5:132202117..132202982,2	Hela-S3	cervix:
6	chr3:101404159..101406579-chr3:101567632..101570275,3	MCF-7	breast:
7	chr3:101405049..101407728-chr3:101567101..101569807,3	K562	blood:
8	chr1:167905772..167906412-chr3:101404998..101405506,2	Hela-S3	cervix:
9	chr3:101403699..101405565-chr3:101445331..101447834,2	K562	blood:
10	chr10:98592030..98592614-chr3:101405121..101405644,2	Hela-S3	cervix:
11	chr3:101280171..101282152-chr3:101404234..101406900,2	MCF-7	breast:
12	chr3:101293011..101294602-chr3:101404209..101407193,2	K562	blood:
13	chr3:101290641..101295184-chr3:101404268..101406806,5	MCF-7	breast:
14	chr11:46615628..46616226-chr3:101405144..101405659,2	Hela-S3	cervix:
15	chr3:101291201..101295304-chr3:101402286..101407928,8	MCF-7	breast:
16	chr3:101404070..101405661-chr3:101567915..101569714,2	MCF-7	breast:
17	chr3:101402329..101408159-chr3:101436960..101445251,11	K562	blood:
18	chr3:101402475..101407282-chr3:101443751..101448081,5	K562	blood:
19	chr3:101403905..101405852-chr3:101497702..101499506,2	MCF-7	breast:
20	chr12:22198711..22199449-chr3:101404905..101405783,2	HCT-116	colon:
21	chr10:112678637..112679593-chr3:101405050..101405570,2	NB4	blood:
22	chr3:101404015..101406572-chr3:101442820..101444519,2	MCF-7	breast:
23	chr3:101405073..101405592-chr8:128747931..128748486,2	Hela-S3	cervix:
24	chr3:101405141..101405682-chr7:45150716..45151680,2	Hela-S3	cervix:
25	chr1:200589537..200590182-chr3:101405310..101405939,2	Hela-S3	cervix:
26	chr20:30194566..30195380-chr3:101405059..101405564,2	Hela-S3	cervix:

Variant related genes	Relation type
RPL24	TF binding region
ENSG00000136935	Chromatin interaction
ENSG00000168028	Chromatin interaction
ENSG00000118193	Chromatin interaction
ENSG00000144802	Chromatin interaction
ENSG00000144815	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000143164	Chromatin interaction
ENSG00000111726	Chromatin interaction
ENSG00000164405	Chromatin interaction
ENSG00000214413	Chromatin interaction
ENSG00000143158	Chromatin interaction
ENSG00000196233	Chromatin interaction
ENSG00000164404	Chromatin interaction
ENSG00000174173	Chromatin interaction
ENSG00000136270	Chromatin interaction
ENSG00000110497	Chromatin interaction
ENSG00000081154	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000108061	Chromatin interaction
ENSG00000182504	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs16844264	1.00[AMR][1000 genomes]
rs56871732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57288874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57768297	1.00[AMR][1000 genomes]
rs58060577	1.00[AMR][1000 genomes]
rs59212280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59610252	1.00[AMR][1000 genomes]
rs59761426	1.00[AMR][1000 genomes]
rs59790563	1.00[AMR][1000 genomes]
rs60451587	1.00[AMR][1000 genomes]
rs60491518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61302621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61468230	1.00[AMR][1000 genomes]
rs61473551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931705	1.00[AMR][1000 genomes]
rs72931709	1.00[AMR][1000 genomes]
rs72931710	1.00[AMR][1000 genomes]
rs72931711	1.00[AMR][1000 genomes]
rs72931715	1.00[AMR][1000 genomes]
rs72931719	1.00[AMR][1000 genomes]
rs72931774	1.00[AMR][1000 genomes]
rs72931789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72933808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72933810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72933821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72933838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72935835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72935839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72935846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72935852	1.00[AMR][1000 genomes]
rs72935865	1.00[AMR][1000 genomes]
rs72935871	1.00[AMR][1000 genomes]
rs72935875	1.00[AMR][1000 genomes]
rs72935894	1.00[AMR][1000 genomes]
rs72937635	1.00[AMR][1000 genomes]
rs72937638	1.00[AMR][1000 genomes]
rs72937639	1.00[AMR][1000 genomes]
rs72937642	1.00[AMR][1000 genomes]
rs72937646	1.00[AMR][1000 genomes]
rs72937653	1.00[AMR][1000 genomes]
rs72937664	1.00[AMR][1000 genomes]
rs72937667	1.00[AMR][1000 genomes]
rs72937684	1.00[AMR][1000 genomes]
rs72937701	1.00[AMR][1000 genomes]
rs72937810	1.00[AMR][1000 genomes]
rs72937817	1.00[AMR][1000 genomes]
rs72939605	1.00[AMR][1000 genomes]
rs72939606	1.00[AMR][1000 genomes]
rs72942266	1.00[AMR][1000 genomes]
rs72942288	1.00[AMR][1000 genomes]
rs72944104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944117	1.00[AMR][1000 genomes]
rs72946006	1.00[AMR][1000 genomes]
rs72946019	1.00[AMR][1000 genomes]
rs72946027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946028	1.00[AMR][1000 genomes]
rs72947370	1.00[AMR][1000 genomes]
rs72947385	1.00[AMR][1000 genomes]
rs72948009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948019	1.00[AMR][1000 genomes]
rs72948050	1.00[AMR][1000 genomes]
rs72948052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72948055	1.00[AMR][1000 genomes]
rs72948056	1.00[AMR][1000 genomes]
rs72948070	1.00[AMR][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101402200-101405400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
2	chr3:101402200-101405400	Transcr. at gene 5' and 3'	A549	lung
3	chr3:101402400-101405600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:101402600-101405400	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr3:101403200-101406000	Active TSS	Psoas Muscle	Psoas
6	chr3:101403200-101406600	Active TSS	Right Ventricle	heart
7	chr3:101403600-101405800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:101403600-101406000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:101403600-101406800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:101403800-101405600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
11	chr3:101403800-101406400	Active TSS	Ovary	ovary
12	chr3:101403800-101406600	Active TSS	Right Atrium	heart
13	chr3:101404200-101406000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:101404200-101406000	Active TSS	Colonic Mucosa	Colon
15	chr3:101404200-101406200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:101404200-101406200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:101404200-101406200	Active TSS	Esophagus	oesophagus
18	chr3:101404200-101406200	Active TSS	Lung	lung
19	chr3:101404200-101406200	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr3:101404200-101406600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr3:101404400-101405400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr3:101404400-101405600	Active TSS	Small Intestine	intestine
23	chr3:101404400-101405600	Bivalent/Poised TSS	HepG2	liver
24	chr3:101404400-101406000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:101404400-101406000	Active TSS	Thymus	Thymus
26	chr3:101404400-101406200	Active TSS	Brain Angular Gyrus	brain
27	chr3:101404400-101406200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:101404400-101406200	Active TSS	Fetal Brain Female	brain
29	chr3:101404400-101406200	Active TSS	Fetal Intestine Large	intestine
30	chr3:101404400-101406200	Active TSS	Placenta Amnion	Placenta Amnion
31	chr3:101404400-101406200	Active TSS	NH-A	brain
32	chr3:101404400-101406400	Active TSS	Fetal Intestine Small	intestine
33	chr3:101404400-101406400	Active TSS	Left Ventricle	heart
34	chr3:101404400-101406400	Active TSS	GM12878-XiMat	blood
35	chr3:101404400-101406600	Active TSS	NHLF	lung
36	chr3:101404400-101406800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr3:101404600-101405600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:101404600-101406000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:101404600-101406000	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr3:101404600-101406000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr3:101404600-101406200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:101404600-101406200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:101404600-101406200	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr3:101404600-101406200	Active TSS	Gastric	stomach
45	chr3:101404600-101406200	Active TSS	Hela-S3	cervix
46	chr3:101404600-101406200	Active TSS	HMEC	breast
47	chr3:101404600-101406200	Active TSS	HSMMtube	muscle
48	chr3:101404600-101406200	Active TSS	HUVEC	blood vessel
49	chr3:101404600-101406200	Active TSS	NHDF-Ad	bronchial
50	chr3:101404600-101406400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links