Variant report

Variant	rs16908827
Chromosome Location	chr10:58121137-58121138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:345)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:345 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:58120501-58122418	GM18505	blood:	n/a	n/a
2	MAFK	chr10:58121078-58121524	HepG2	liver:	n/a	n/a
3	POLR2A	chr10:58120677-58121545	PANC-1	pancreas:	n/a	n/a
4	ELK1	chr10:58121013-58121433	K562	blood:	n/a	n/a
5	REST	chr10:58120740-58121762	HL-60	blood:	n/a	n/a
6	TAF1	chr10:58120686-58121462	PFSK-1	brain:	n/a	n/a
7	MYC	chr10:58120748-58121824	K562	blood:	n/a	n/a
8	POLR2A	chr10:58120696-58121621	HUVEC	blood vessel:	n/a	n/a
9	FOXA1	chr10:58120859-58121271	T-47D	breast:	n/a	n/a
10	ZKSCAN1	chr10:58120926-58121318	Hela-S3	cervix:	n/a	n/a
11	YY1	chr10:58120663-58121262	ECC-1	luminal epithelium:	n/a	chr10:58120989-58121001
12	NRF1	chr10:58121005-58121484	Hela-S3	cervix:	n/a	chr10:58121211-58121222 chr10:58121173-58121184 chr10:58121211-58121222 chr10:58121174-58121185 chr10:58121211-58121225 chr10:58121213-58121222 chr10:58121174-58121188 chr10:58121208-58121222 chr10:58121197-58121208
13	POLR2A	chr10:58120653-58121424	MCF-7	breast:	n/a	n/a
14	POU2F2	chr10:58120749-58121172	GM12891	blood:	n/a	n/a
15	POLR2A	chr10:58120453-58121885	GM12892	blood:	n/a	n/a
16	CHD2	chr10:58120761-58121379	K562	blood:	n/a	n/a
17	POLR2A	chr10:58120155-58121896	GM19099	blood:	n/a	n/a
18	GATA3	chr10:58120872-58121877	T-47D	breast:	n/a	n/a
19	POLR2A	chr10:58120530-58121416	GM12892	blood:	n/a	n/a
20	JUND	chr10:58120721-58121821	K562	blood:	n/a	n/a
21	HA-E2F1	chr10:58120644-58121401	Hela-S3	cervix:	n/a	chr10:58121175-58121184 chr10:58121080-58121089 chr10:58121212-58121221
22	ZC3H11A	chr10:58120871-58121452	K562	blood:	n/a	n/a
23	MXI1	chr10:58120500-58122080	SK-N-SH	brain:	n/a	n/a
24	HEY1	chr10:58120814-58121388	HepG2	liver:	n/a	chr10:58120920-58120935
25	POLR2A	chr10:58120817-58121491	H1-neurons	neurons:	n/a	n/a
26	ARID3A	chr10:58121064-58121489	HepG2	liver:	n/a	chr10:58121356-58121372
27	POLR2A	chr10:58120674-58121442	GM12891	blood:	n/a	n/a
28	ZNF143	chr10:58120814-58121529	K562	blood:	n/a	chr10:58121021-58121040 chr10:58121069-58121079 chr10:58121024-58121039
29	ELF1	chr10:58120621-58121334	GM12878	blood:	n/a	chr10:58120920-58120932
30	SIN3AK20	chr10:58120860-58121139	SK-N-SH	brain:	n/a	n/a
31	STAT5A	chr10:58120709-58121517	GM12878	blood:	n/a	n/a
32	YY1	chr10:58120776-58121205	NT2-D1	testis:	n/a	chr10:58120989-58121001
33	POLR2A	chr10:58121115-58121427	HepG2	liver:	n/a	n/a
34	SP2	chr10:58120901-58121227	H1-hESC	embryonic stem cell:	n/a	chr10:58121094-58121109
35	RAD21	chr10:58120661-58121602	Hela-S3	cervix:	n/a	chr10:58120921-58120934
36	TAF1	chr10:58120540-58121760	ECC-1	luminal epithelium:	n/a	n/a
37	HMGN3	chr10:58120842-58121324	K562	blood:	n/a	n/a
38	POLR2A	chr10:58119390-58122767	GM12891	blood:	n/a	n/a
39	CHD2	chr10:58120751-58121522	H1-hESC	embryonic stem cell:	n/a	n/a
40	MYC	chr10:58121030-58121624	MCF10A-Er-Src	breast:	n/a	n/a
41	POU2F2	chr10:58120700-58121364	GM12878	blood:	n/a	n/a
42	RFX5	chr10:58120906-58121299	HepG2	liver:	n/a	n/a
43	CREB1	chr10:58120912-58121262	A549	lung:	n/a	n/a
44	SP1	chr10:58120824-58121397	H1-hESC	embryonic stem cell:	n/a	chr10:58121098-58121109
45	MAX	chr10:58120816-58121455	GM12878	blood:	n/a	n/a
46	SETDB1	chr10:58120857-58121459	U2OS	brain:	n/a	chr10:58121212-58121221 chr10:58121175-58121184
47	REST	chr10:58120795-58121557	A549	lung:	n/a	n/a
48	MAX	chr10:58120682-58121587	A549	lung:	n/a	n/a
49	YY1	chr10:58120769-58121225	SK-N-SH_RA	brain:	n/a	chr10:58120989-58121001
50	MTA3	chr10:58120263-58121795	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:58121125-58121175	BJ	skin:	n/a
2	chr10:58121125-58121175	AG04450	lung:	fetal
3	chr10:58121125-58121175	PFSK-1	brain:	n/a
4	chr10:58121125-58121175	HEEpiC	esophagus:	n/a
5	chr10:58121125-58121175	BE2_C	brain:	n/a
6	chr10:58121125-58121175	GM06990	blood:	n/a
7	chr10:58121125-58121175	Caco-2	colon:	n/a
8	chr10:58121125-58121175	NB4	blood:	n/a
9	chr10:58121125-58121175	SK-N-SH	brain:	n/a
10	chr10:58121125-58121175	HNPCEpiC	eye:	n/a
11	chr10:58121125-58121175	NH-A	brain:	n/a
12	chr10:58121125-58121175	ProgFib	skin:	n/a
13	chr10:58121125-58121175	HCT-116	colon:	n/a
14	chr10:58121125-58121175	NHBE	bronchial:	n/a
15	chr10:58121125-58121175	AG10803	skin:	n/a
16	chr10:58121125-58121175	PrEC	prostate:	n/a
17	chr10:58121125-58121175	GM12892	blood:	n/a
18	chr10:58121125-58121175	GM12878	blood:	n/a
19	chr10:58121125-58121175	H1-hESC	embryonic stem cell:	embryo
20	chr10:58121125-58121175	AG04449	skin:	fetal
21	chr10:58121125-58121175	Hepatocyte	liver:	n/a
22	chr10:58121125-58121175	AG09309	skin:	n/a
23	chr10:58121125-58121175	MCF-7	breast:	n/a
24	chr10:58121125-58121175	HCM	heart:	n/a
25	chr10:58121125-58121175	NT2-D1	testis:	n/a
26	chr10:58121125-58121175	GM12891	blood:	n/a
27	chr10:58121125-58121175	ECC-1	luminal epithelium:	n/a
28	chr10:58121125-58121175	HEK293	kidney:	embryo
29	chr10:58121125-58121175	PANC-1	pancreas:	n/a
30	chr10:58121125-58121175	HPAEpiC	pulmonary alveolar:	n/a
31	chr10:58121125-58121175	NHDF-neo	bronchial:	n/a
32	chr10:58121125-58121175	Hela-S3	cervix:	n/a
33	chr10:58121125-58121175	HCPEpiC	choroid plexus:	n/a
34	chr10:58121125-58121175	HepG2	liver:	n/a
35	chr10:58121125-58121175	ovcar-3	ovarian:	n/a
36	chr10:58121125-58121175	RPTEC	kidney:	n/a
37	chr10:58121125-58121175	HRPEpiC	eye:	n/a
38	chr10:58121125-58121175	HL-60	blood:	n/a
39	chr10:58121125-58121175	SKMC	muscle:	n/a
40	chr10:58121125-58121175	T-47D	breast:	n/a
41	chr10:58121125-58121175	CMK	blood:	n/a
42	chr10:58121125-58121175	LNCaP	prostate:	n/a
43	chr10:58121125-58121175	HMEC	breast:	n/a
44	chr10:58121125-58121175	A549	lung:	n/a
45	chr10:58121125-58121175	K562	blood:	n/a
46	chr10:58121125-58121175	IMR90	lung:	fetal
47	chr10:58121125-58121175	U87	brain:	n/a
48	chr10:58121125-58121175	MCF10A-Er-Src	breast:	n/a
49	chr10:58121125-58121175	SK-N-MC	brain:	n/a
50	chr10:58121125-58121175	HUVEC	blood vessel:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:58121092..58124611-chr10:58124835..58127266,3	K562	blood:
2	chr10:58121131..58123400-chr10:58127785..58130133,3	MCF-7	breast:
3	chr10:58120970..58121505-chr9:128468991..128469616,2	HCT-116	colon:
4	chr10:58120889..58121499-chr15:42565318..42565842,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ZWINT	TF binding region
ZWINT	CpG island
ENSG00000103978	Chromatin interaction
ENSG00000119487	Chromatin interaction
ENSG00000214013	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16908833	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16908837	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58358142	1.00[AMR][1000 genomes]
rs60761978	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73281989	1.00[AMR][1000 genomes]
rs73281991	1.00[AMR][1000 genomes]
rs73281992	1.00[AMR][1000 genomes]
rs73281994	1.00[AMR][1000 genomes]
rs73281997	1.00[AMR][1000 genomes]
rs73281998	1.00[AMR][1000 genomes]
rs73283614	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283620	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283621	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283625	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73283693	1.00[AMR][1000 genomes]
rs73283823	1.00[AMR][1000 genomes]
rs73285910	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752691	chr10:57738694-58541894	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv831883	chr10:57947759-58139056	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv895503	chr10:58029209-58201703	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895504	chr10:58029209-58230622	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1035842	chr10:58084841-58150135	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16908827	FAM153A	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:58119800-58122000	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr10:58119800-58122000	Active TSS	NHLF	lung
3	chr10:58120000-58121600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:58120000-58122000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr10:58120000-58122000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr10:58120000-58122000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr10:58120000-58122000	Active TSS	Fetal Kidney	kidney
8	chr10:58120000-58122000	Active TSS	Rectal Smooth Muscle	rectum
9	chr10:58120000-58122400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:58120000-58122400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr10:58120200-58121600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr10:58120200-58122000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr10:58120200-58122000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:58120200-58122000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr10:58120200-58122000	Active TSS	A549	lung
16	chr10:58120200-58122000	Active TSS	NHDF-Ad	bronchial
17	chr10:58120200-58122200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr10:58120200-58122400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:58120200-58122400	Active TSS	GM12878-XiMat	blood
20	chr10:58120200-58122800	Active TSS	K562	blood
21	chr10:58120400-58121800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr10:58120400-58121800	Active TSS	Brain Cingulate Gyrus	brain
23	chr10:58120400-58121800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr10:58120400-58121800	Active TSS	Sigmoid Colon	Sigmoid Colon
25	chr10:58120400-58122000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr10:58120400-58122000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr10:58120400-58122000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:58120400-58122000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr10:58120400-58122000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr10:58120400-58122000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr10:58120400-58122000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:58120400-58122000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:58120400-58122000	Active TSS	Brain Substantia Nigra	brain
34	chr10:58120400-58122000	Active TSS	Colonic Mucosa	Colon
35	chr10:58120400-58122000	Active TSS	Fetal Intestine Small	intestine
36	chr10:58120400-58122000	Active TSS	Fetal Lung	lung
37	chr10:58120400-58122000	Active TSS	Placenta Amnion	Placenta Amnion
38	chr10:58120400-58122000	Active TSS	Right Atrium	heart
39	chr10:58120400-58122000	Active TSS	Hela-S3	cervix
40	chr10:58120400-58122000	Active TSS	HSMM	muscle
41	chr10:58120400-58122000	Active TSS	HSMMtube	muscle
42	chr10:58120400-58122400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:58120400-58122400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:58120400-58122400	Active TSS	HMEC	breast
45	chr10:58120400-58122600	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr10:58120600-58121400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr10:58120600-58121400	Active TSS	HepG2	liver
48	chr10:58120600-58121600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr10:58120600-58121600	Active TSS	Placenta	Placenta
50	chr10:58120600-58121600	Active TSS	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links