Variant report

Variant	rs3813609
Chromosome Location	chr1:161019040-161019041
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161018755-161019112	HepG2	liver:	n/a	n/a
2	ZNF274	chr1:161019010-161019817	NT2-D1	testis:	n/a	n/a
3	MTA3	chr1:161018867-161019322	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:161014643-161019294	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:161018701-161019220	GM12891	blood:	n/a	n/a
6	POLR2A	chr1:161018733-161019744	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:161017188-161019650	HL-60	blood:	n/a	n/a
8	POLR2A	chr1:161014545-161019636	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:161014539-161020077	GM12891	blood:	n/a	n/a
10	ZNF274	chr1:161019030-161019625	GM08714	blood:	n/a	n/a
11	POLR2A	chr1:161014679-161019283	GM12891	blood:	n/a	n/a
12	ZNF263	chr1:161018683-161019519	HEK293-T-REx	kidney:	n/a	n/a
13	POLR2A	chr1:161014590-161019264	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:161018664-161019388	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:161018988-161019294	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr1:161018668-161019608	GM12878	blood:	n/a	n/a
17	ZNF274	chr1:161018998-161019908	K562	blood:	n/a	n/a
18	POLR2A	chr1:161018981-161019087	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:160965107..160967123-chr1:161018782..161021042,2	MCF-7	breast:
2	chr1:161013435..161019346-chr1:161039308..161043996,7	MCF-7	breast:
3	chr1:161017585..161019978-chr1:161027993..161031317,3	MCF-7	breast:
4	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
5	chr1:161013674..161020196-chr1:161084642..161090709,10	MCF-7	breast:
6	chr1:161018354..161021283-chr1:161024769..161026655,3	K562	blood:
7	chr1:160989721..160993044-chr1:161014364..161019082,7	K562	blood:
8	chr1:161018427..161020724-chr1:161039039..161040672,2	K562	blood:

No data

Variant related genes	Relation type
USF1	TF binding region
ENSG00000158769	Chromatin interaction
ENSG00000186517	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000143256	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11576837	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12728349	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12748157	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073657	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774273	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212386	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3813609	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016200-161022600	Weak transcription	Gastric	stomach
2	chr1:161016400-161020800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:161016400-161022600	Weak transcription	Small Intestine	intestine
4	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
5	chr1:161016600-161019400	ZNF genes & repeats	Fetal Stomach	stomach
6	chr1:161016600-161020200	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr1:161016600-161022200	Weak transcription	Brain Anterior Caudate	brain
8	chr1:161016600-161024200	Weak transcription	Right Ventricle	heart
9	chr1:161016600-161028000	Weak transcription	Brain Substantia Nigra	brain
10	chr1:161016800-161021800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:161016800-161029200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:161017000-161019400	Genic enhancers	Primary B cells from peripheral blood	blood
13	chr1:161017000-161022000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:161017000-161024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:161017000-161029400	Strong transcription	Primary T cells from cord blood	blood
16	chr1:161017000-161031600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:161017200-161019400	Genic enhancers	Spleen	Spleen
19	chr1:161017200-161020000	Genic enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:161017200-161021200	Weak transcription	Stomach Mucosa	stomach
21	chr1:161017200-161022000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:161017200-161029200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:161017200-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:161017400-161019600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:161017400-161019600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:161017400-161022600	Weak transcription	K562	blood
27	chr1:161017400-161027400	Strong transcription	Primary hematopoietic stem cells	blood
28	chr1:161017400-161027400	Strong transcription	Dnd41	blood
29	chr1:161017400-161030000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:161017400-161031000	Strong transcription	Thymus	Thymus
31	chr1:161017600-161021000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr1:161017600-161024000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:161017600-161034400	Strong transcription	Fetal Thymus	thymus
34	chr1:161017800-161019400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:161017800-161019800	ZNF genes & repeats	Liver	Liver
36	chr1:161017800-161020000	Strong transcription	Esophagus	oesophagus
37	chr1:161017800-161024400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:161017800-161026200	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:161018000-161019800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr1:161018000-161025800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:161018000-161027400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:161018200-161026800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:161018400-161026000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:161018400-161026400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:161018400-161027400	Strong transcription	GM12878-XiMat	blood
46	chr1:161018600-161020000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:161018600-161024200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:161018600-161032400	Strong transcription	Primary B cells from cord blood	blood
49	chr1:161018600-161033600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:161018800-161019200	Enhancers	Pancreas	Pancrea

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