Variant report

Variant	rs12116949
Chromosome Location	chr1:161042063-161042064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:161041960-161042110	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr1:161041428-161042236	A549	lung:	n/a	n/a
3	RAD21	chr1:161041499-161042217	HCT-116	colon:	n/a	n/a
4	CCNT2	chr1:161041853-161042239	K562	blood:	n/a	n/a
5	RAD21	chr1:161041515-161042089	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:161042061-161042205	GM19239	blood:	n/a	n/a
7	FOXA2	chr1:161041560-161042078	A549	lung:	n/a	n/a
8	RAD21	chr1:161041625-161042282	HCT-116	colon:	n/a	n/a
9	RUNX3	chr1:161041902-161042210	GM12878	blood:	n/a	n/a
10	SMC3	chr1:161041604-161042132	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr1:161041443-161042337	HCT-116	colon:	n/a	n/a
12	CTCF	chr1:161042040-161042190	GM12870	blood:	n/a	n/a
13	MAX	chr1:161041660-161042122	NB4	blood:	n/a	n/a
14	CTCF	chr1:161042000-161042150	GM12875	blood:	n/a	n/a
15	SMC3	chr1:161041635-161042151	SK-N-SH	brain:	n/a	n/a
16	MAX	chr1:161041655-161043335	HepG2	liver:	n/a	n/a
17	CTCF	chr1:161041645-161042108	MCF-7	breast:	n/a	n/a
18	MAX	chr1:161041647-161042064	K562	blood:	n/a	n/a
19	RAD21	chr1:161041566-161042079	ECC-1	luminal epithelium:	n/a	n/a
20	RAD21	chr1:161041671-161042094	MCF-7	breast:	n/a	n/a
21	RAD21	chr1:161041641-161042100	A549	lung:	n/a	n/a
22	CTCF	chr1:161041637-161042064	K562	blood:	n/a	n/a
23	CTCF	chr1:161041530-161042272	SK-N-SH	brain:	n/a	n/a
24	MTA3	chr1:161041688-161042175	GM12878	blood:	n/a	n/a
25	CTCF	chr1:161041980-161042130	GM12867	blood:	n/a	n/a
26	RAD21	chr1:161041479-161042198	SK-N-SH	brain:	n/a	n/a
27	RAD21	chr1:161041611-161042160	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:161042063-161042113	NHDF-neo	bronchial:	n/a
2	chr1:161042063-161042113	AG04450	lung:	fetal
3	chr1:161042063-161042113	IMR90	lung:	fetal
4	chr1:161042063-161042113	HEEpiC	esophagus:	n/a
5	chr1:161042063-161042113	SK-N-SH	brain:	n/a
6	chr1:161042063-161042113	GM12878	blood:	n/a
7	chr1:161042063-161042113	HMEC	breast:	n/a
8	chr1:161042063-161042113	HIPEpiC	eye:	n/a
9	chr1:161042063-161042113	NT2-D1	testis:	n/a
10	chr1:161042063-161042113	Hepatocyte	liver:	n/a
11	chr1:161042063-161042113	ovcar-3	ovarian:	n/a
12	chr1:161042063-161042113	SAEC	small airway:	n/a
13	chr1:161042063-161042113	H1-hESC	embryonic stem cell:	embryo
14	chr1:161042063-161042113	GM12891	blood:	n/a
15	chr1:161042063-161042113	U87	brain:	n/a
16	chr1:161042063-161042113	AG09309	skin:	n/a
17	chr1:161042063-161042113	Hela-S3	cervix:	n/a
18	chr1:161042063-161042113	AG09319	gingival:	n/a
19	chr1:161042063-161042113	HCM	heart:	n/a
20	chr1:161042063-161042113	AG04449	skin:	fetal
21	chr1:161042063-161042113	GM06990	blood:	n/a
22	chr1:161042063-161042113	A549	lung:	n/a
23	chr1:161042063-161042113	PANC-1	pancreas:	n/a
24	chr1:161042063-161042113	SK-N-SH_RA	brain:	n/a
25	chr1:161042063-161042113	ProgFib	skin:	n/a
26	chr1:161042063-161042113	HCT-116	colon:	n/a
27	chr1:161042063-161042113	HRPEpiC	eye:	n/a
28	chr1:161042063-161042113	CMK	blood:	n/a
29	chr1:161042063-161042113	K562	blood:	n/a
30	chr1:161042063-161042113	Jurkat	blood:	n/a
31	chr1:161042063-161042113	AG10803	skin:	n/a
32	chr1:161042063-161042113	PrEC	prostate:	n/a
33	chr1:161042063-161042113	GM19239	blood:	n/a
34	chr1:161042063-161042113	BE2_C	brain:	n/a
35	chr1:161042063-161042113	ECC-1	luminal epithelium:	n/a
36	chr1:161042063-161042113	BJ	skin:	n/a
37	chr1:161042063-161042113	NH-A	brain:	n/a
38	chr1:161042063-161042113	HPAEpiC	pulmonary alveolar:	n/a
39	chr1:161042063-161042113	NB4	blood:	n/a
40	chr1:161042063-161042113	HCF	heart:	n/a
41	chr1:161042063-161042113	MCF10A-Er-Src	breast:	n/a
42	chr1:161042063-161042113	NHBE	bronchial:	n/a
43	chr1:161042063-161042113	RPTEC	kidney:	n/a
44	chr1:161042063-161042113	HL-60	blood:	n/a
45	chr1:161042063-161042113	HNPCEpiC	eye:	n/a
46	chr1:161042063-161042113	HRE	kidney:	n/a
47	chr1:161042063-161042113	HAEpiC	amniotic membrane:	n/a
48	chr1:161042063-161042113	PFSK-1	brain:	n/a
49	chr1:161042063-161042113	T-47D	breast:	n/a
50	chr1:161042063-161042113	GM12892	blood:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
2	chr1:161041327..161042169-chr1:161066813..161068080,6	MCF-7	breast:
3	chr1:161040956..161045180-chr1:161134527..161136918,3	MCF-7	breast:
4	chr1:160982248..160985015-chr1:161041891..161043731,2	K562	blood:
5	chr1:161041307..161042464-chr1:161067079..161068224,19	MCF-7	breast:
6	chr1:161041431..161042257-chr1:161128491..161129236,2	K562	blood:
7	chr1:161035244..161038070-chr1:161039157..161043697,5	MCF-7	breast:
8	chr1:161041322..161042651-chr1:161108963..161110253,9	K562	blood:

No data

Variant related genes	Relation type
ARHGAP30	TF binding region
ARHGAP30	CpG island
ENSG00000162755	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000143224	Chromatin interaction
ENSG00000224985	Chromatin interaction
ENSG00000268154	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11265544	0.82[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap]
rs11588189	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs12130871	1.00[JPT][hapmap]
rs12135996	0.95[ASN][1000 genomes]
rs12721035	1.00[LWK][hapmap]
rs16832733	1.00[LWK][hapmap]
rs2184065	1.00[LWK][hapmap]
rs2516838	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs2774279	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs3892375	0.82[ASW][hapmap];0.83[AMR][1000 genomes]
rs6413453	1.00[LWK][hapmap]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv947135	chr1:161041002-161050287	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12116949	USF1	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161030000-161046200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:161038800-161043400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:161039000-161043400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:161039200-161042400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:161039600-161049000	Weak transcription	Lung	lung
6	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
7	chr1:161039800-161049000	Weak transcription	Fetal Intestine Small	intestine
8	chr1:161039800-161052600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:161039800-161053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:161040000-161042200	Enhancers	Primary B cells from peripheral blood	blood
11	chr1:161040000-161042400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr1:161040000-161044400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:161040200-161042200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr1:161040200-161042200	Enhancers	Primary B cells from cord blood	blood
15	chr1:161040200-161042200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:161040200-161042200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:161040200-161042400	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:161040200-161042400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:161040200-161042400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:161040200-161042400	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr1:161040200-161042600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:161040200-161042600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:161040200-161045000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr1:161040200-161052600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:161040200-161052800	Weak transcription	Colonic Mucosa	Colon
26	chr1:161040400-161042200	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:161040600-161042200	Enhancers	Primary T cells from cord blood	blood
28	chr1:161040800-161042200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:161040800-161042200	Weak transcription	Stomach Mucosa	stomach
30	chr1:161040800-161042400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:161040800-161046800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:161041000-161043200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:161041200-161043000	Weak transcription	HMEC	breast
34	chr1:161041200-161043600	Genic enhancers	Placenta	Placenta
35	chr1:161041400-161043200	Weak transcription	NHEK	skin
36	chr1:161041800-161042200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:161041800-161042200	Enhancers	Adipose Nuclei	Adipose
38	chr1:161041800-161042200	Enhancers	Hela-S3	cervix
39	chr1:161041800-161042200	Enhancers	K562	blood
40	chr1:161041800-161042400	Enhancers	Fetal Muscle Trunk	muscle
41	chr1:161041800-161043400	Flanking Active TSS	HepG2	liver
42	chr1:161041800-161043800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:161042000-161042200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:161042000-161042200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr1:161042000-161042200	Flanking Active TSS	Spleen	Spleen
46	chr1:161042000-161042200	Enhancers	HSMM	muscle
47	chr1:161042000-161042600	Strong transcription	Fetal Stomach	stomach
48	chr1:161042000-161043000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:161042000-161043400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr1:161042000-161043400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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