Variant report

Variant	rs2774279
Chromosome Location	chr1:161017556-161017557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161017450-161018431	GM19193	blood:	n/a	n/a
2	POLR2A	chr1:161014678-161018455	GM18505	blood:	n/a	n/a
3	POLR2A	chr1:161017555-161017685	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:161014603-161018080	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:161014375-161017763	GM12878	blood:	n/a	n/a
6	MTA3	chr1:161014325-161017601	GM12878	blood:	n/a	n/a
7	GTF2F1	chr1:161017472-161017564	K562	blood:	n/a	n/a
8	POLR2A	chr1:161017311-161017679	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:161014475-161018415	GM12892	blood:	n/a	n/a
10	STAT5A	chr1:161017239-161017719	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:161014643-161019294	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:161014905-161017696	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:161014559-161018477	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:161016975-161017685	K562	blood:	n/a	n/a
15	POLR2A	chr1:161017188-161019650	HL-60	blood:	n/a	n/a
16	POLR2A	chr1:161014545-161019636	GM12892	blood:	n/a	n/a
17	POLR2A	chr1:161017224-161018394	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr1:161017399-161017806	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:161014539-161020077	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:161014613-161017593	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:161017303-161018367	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:161014682-161017621	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr1:161014662-161018344	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:161014845-161017752	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr1:161014679-161019283	GM12891	blood:	n/a	n/a
26	POLR2A	chr1:161014590-161019264	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:161017354-161018324	HepG2	liver:	n/a	n/a
28	USF2	chr1:161015531-161017612	Hela-S3	cervix:	n/a	n/a
29	GTF2F1	chr1:161014764-161017628	Hela-S3	cervix:	n/a	n/a
30	NFATC1	chr1:161015244-161017561	GM12878	blood:	n/a	n/a
31	PML	chr1:161014226-161017644	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:161017259-161018462	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:161015505-161018048	K562	blood:	n/a	n/a
34	POLR2A	chr1:161014934-161018363	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:161017237-161017945	K562	blood:	n/a	n/a
36	POLR2A	chr1:161014551-161017681	GM12891	blood:	n/a	n/a
37	POLR2A	chr1:161017390-161017877	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161016360..161018809-chr1:161057728..161060348,2	MCF-7	breast:
2	chr1:160990576..160992373-chr1:161014612..161018487,6	K562	blood:
3	chr1:161013470..161017562-chr1:161084888..161088962,4	MCF-7	breast:
4	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
5	chr1:161016538..161018729-chr1:161068752..161071676,2	K562	blood:
6	chr1:161013542..161018278-chr1:161100825..161104206,7	MCF-7	breast:
7	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
8	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
9	chr1:161015316..161018134-chr1:161085942..161088191,3	K562	blood:
10	chr1:161016767..161018493-chr1:161123152..161124875,2	K562	blood:
11	chr1:161014200..161017793-chr1:161057956..161063190,6	MCF-7	breast:
12	chr1:160986487..160988854-chr1:161017153..161018822,2	MCF-7	breast:
13	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
14	chr1:161013674..161020196-chr1:161084642..161090709,10	MCF-7	breast:
15	chr1:161015894..161017735-chr21:33302300..33304162,2	MCF-7	breast:
16	chr1:161015820..161018500-chr14:21736377..21738014,2	MCF-7	breast:
17	chr1:161011339..161013490-chr1:161016100..161018968,3	K562	blood:
18	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
19	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:

No data

Variant related genes	Relation type
USF1	TF binding region
ENSG00000158773	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000186517	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000143222	Chromatin interaction
ENSG00000092199	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158796	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11265544	1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11588189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12116949	0.85[CHB][hapmap];0.92[CHD][hapmap]
rs12130871	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2516838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34339899	0.83[ASN][1000 genomes]
rs35925761	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3892375	0.82[JPT][hapmap]
rs4656974	0.90[ASN][1000 genomes]
rs4656977	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2774279	KIRREL	cis	parietal	SCAN
rs2774279	USF1	cis	lymphoblastoid	seeQTL
rs2774279	ITLN1	cis	cerebellum	SCAN
rs2774279	OR10K1	cis	cerebellum	SCAN
rs2774279	SNORA42	cis	cerebellum	SCAN
rs2774279	FCGR2A	cis	parietal	SCAN
rs2774279	PEAR1	cis	cerebellum	SCAN
rs2774279	F11R	cis	cerebellum	SCAN
rs2774279	FCRL1	cis	cerebellum	SCAN
rs2774279	ARHGEF11	cis	cerebellum	SCAN
rs2774279	USF1	cis	multi-tissue	Pritchard

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016200-161022600	Weak transcription	Gastric	stomach
2	chr1:161016400-161017600	Weak transcription	Aorta	Aorta
3	chr1:161016400-161017800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:161016400-161017800	Weak transcription	Esophagus	oesophagus
5	chr1:161016400-161018200	Enhancers	Placenta	Placenta
6	chr1:161016400-161018600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:161016400-161018800	Weak transcription	Pancreas	Pancrea
8	chr1:161016400-161018800	Weak transcription	Right Atrium	heart
9	chr1:161016400-161020800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:161016400-161022600	Weak transcription	Small Intestine	intestine
11	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
12	chr1:161016600-161017600	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr1:161016600-161017600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:161016600-161017600	Enhancers	Adipose Nuclei	Adipose
15	chr1:161016600-161017600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr1:161016600-161018800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:161016600-161019400	ZNF genes & repeats	Fetal Stomach	stomach
18	chr1:161016600-161020200	ZNF genes & repeats	Fetal Intestine Small	intestine
19	chr1:161016600-161022200	Weak transcription	Brain Anterior Caudate	brain
20	chr1:161016600-161024200	Weak transcription	Right Ventricle	heart
21	chr1:161016600-161028000	Weak transcription	Brain Substantia Nigra	brain
22	chr1:161016800-161017600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:161016800-161017600	ZNF genes & repeats	A549	lung
24	chr1:161016800-161017800	Weak transcription	Liver	Liver
25	chr1:161016800-161018000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:161016800-161018400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr1:161016800-161018800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr1:161016800-161018800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:161016800-161021800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr1:161016800-161029200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:161017000-161017600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:161017000-161017600	Weak transcription	Fetal Thymus	thymus
33	chr1:161017000-161017800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:161017000-161017800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:161017000-161017800	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr1:161017000-161018000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:161017000-161018200	Enhancers	Primary B cells from cord blood	blood
38	chr1:161017000-161018200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:161017000-161018200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
40	chr1:161017000-161019400	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr1:161017000-161022000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:161017000-161024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:161017000-161029400	Strong transcription	Primary T cells from cord blood	blood
44	chr1:161017000-161031600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr1:161017200-161018400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:161017200-161019400	Genic enhancers	Spleen	Spleen
48	chr1:161017200-161020000	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr1:161017200-161021200	Weak transcription	Stomach Mucosa	stomach
50	chr1:161017200-161022000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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