Variant report

Variant	rs3811621
Chromosome Location	chr2:190446541-190446542
allele	C/G
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	CEBPB	chr2:190446508-190446996	K562	blood:	n/a	n/a
2	STAT5A	chr2:190446477-190447123	K562	blood:	n/a	n/a
3	IRF1	chr2:190446465-190447740	K562	blood:	n/a	chr2:190447593-190447606 chr2:190447595-190447606 chr2:190447587-190447600 chr2:190447589-190447603 chr2:190447586-190447603 chr2:190447595-190447605 chr2:190447589-190447599 chr2:190447595-190447609 chr2:190447591-190447605 chr2:190447593-190447606 chr2:190447587-190447607
4	TAL1	chr2:190445583-190447295	K562	blood:	n/a	chr2:190446828-190446846
5	HMGN3	chr2:190445150-190446945	K562	blood:	n/a	n/a
6	RAD21	chr2:190446152-190446750	H1-hESC	embryonic stem cell:	n/a	n/a
7	TEAD4	chr2:190446031-190446791	H1-hESC	embryonic stem cell:	n/a	n/a
8	SMC3	chr2:190446463-190446632	HepG2	liver:	n/a	n/a
9	EP300	chr2:190446535-190447438	K562	blood:	n/a	chr2:190447363-190447377 chr2:190446895-190446909
10	CEBPD	chr2:190446458-190447127	K562	blood:	n/a	n/a
11	CEBPB	chr2:190446380-190446764	H1-hESC	embryonic stem cell:	n/a	n/a
12	TBP	chr2:190444906-190447343	K562	blood:	n/a	n/a
13	CTBP2	chr2:190444952-190446826	H1-hESC	embryonic stem cell:	n/a	n/a
14	HCFC1	chr2:190446514-190446909	K562	blood:	n/a	n/a
15	TBL1XR1	chr2:190446237-190447099	K562	blood:	n/a	n/a
16	TEAD4	chr2:190446366-190447263	K562	blood:	n/a	n/a
17	MYC	chr2:190446140-190447379	K562	blood:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
18	EP300	chr2:190446006-190447605	K562	blood:	n/a	chr2:190447570-190447584 chr2:190447363-190447377 chr2:190446895-190446909 chr2:190447590-190447604
19	YY1	chr2:190446523-190446945	K562	blood:	n/a	n/a
20	CCNT2	chr2:190445363-190446970	K562	blood:	n/a	chr2:190446828-190446848 chr2:190446371-190446380
21	PML	chr2:190446169-190447123	K562	blood:	n/a	n/a
22	REST	chr2:190446317-190446585	K562	blood:	n/a	chr2:190446465-190446474 chr2:190446454-190446472
23	GATA2	chr2:190446516-190446982	K562	blood:	n/a	chr2:190446835-190446848 chr2:190446838-190446846 chr2:190446828-190446845
24	POLR2A	chr2:190444982-190447214	K562	blood:	n/a	n/a
25	TBL1XR1	chr2:190446207-190447408	K562	blood:	n/a	n/a
26	BHLHE40	chr2:190446396-190447514	K562	blood:	n/a	n/a
27	ZMIZ1	chr2:190445083-190447504	K562	blood:	n/a	n/a
28	CEBPD	chr2:190446486-190447054	K562	blood:	n/a	n/a
29	RXRA	chr2:190446273-190446616	H1-hESC	embryonic stem cell:	n/a	n/a
30	TEAD4	chr2:190446008-190447221	K562	blood:	n/a	n/a
31	GATA3	chr2:190446268-190446898	T-47D	breast:	n/a	chr2:190446835-190446848 chr2:190446838-190446846 chr2:190446828-190446845
32	POLR2A	chr2:190444897-190447250	K562	blood:	n/a	n/a
33	NR2F2	chr2:190445997-190447163	K562	blood:	n/a	n/a
34	POLR2A	chr2:190444227-190448816	PBDE	blood:	n/a	n/a
35	GATA1	chr2:190444265-190447639	PBDE	blood:	n/a	chr2:190446835-190446848 chr2:190444336-190444343 chr2:190446838-190446846 chr2:190444485-190444495 chr2:190446828-190446845
36	RCOR1	chr2:190444861-190447429	K562	blood:	n/a	n/a
37	POLR2A	chr2:190445009-190447207	K562	blood:	n/a	n/a
38	SP1	chr2:190446034-190446642	H1-hESC	embryonic stem cell:	n/a	chr2:190446369-190446380 chr2:190446370-190446379 chr2:190446370-190446379 chr2:190446370-190446380 chr2:190446371-190446380 chr2:190446370-190446380 chr2:190446369-190446381 chr2:190446369-190446381 chr2:190446370-190446384 chr2:190446601-190446608
39	MAFK	chr2:190446445-190447420	K562	blood:	n/a	chr2:190447332-190447343 chr2:190447332-190447343 chr2:190447327-190447343 chr2:190447331-190447342 chr2:190447322-190447342 chr2:190447330-190447344
40	POLR2A	chr2:190444989-190447536	K562	blood:	n/a	n/a
41	MAX	chr2:190446495-190446953	K562	blood:	n/a	n/a
42	PML	chr2:190446374-190447082	K562	blood:	n/a	n/a
43	RCOR1	chr2:190446091-190446581	HepG2	liver:	n/a	n/a
44	TAF1	chr2:190446524-190446957	K562	blood:	n/a	n/a
45	UBTF	chr2:190445058-190447034	K562	blood:	n/a	n/a
46	RCOR1	chr2:190446177-190447180	K562	blood:	n/a	n/a
47	MAZ	chr2:190444975-190447075	K562	blood:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
48	MAX	chr2:190444828-190446842	HepG2	liver:	n/a	chr2:190446376-190446385 chr2:190446372-190446382
49	HEY1	chr2:190446048-190447010	K562	blood:	n/a	n/a
50	HEY1	chr2:190444877-190446966	K562	blood:	n/a	chr2:190445659-190445674 chr2:190445648-190445663

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:190446494-190446544	NB4	blood:	n/a
2	chr2:190446494-190446544	HRE	kidney:	n/a
3	chr2:190446494-190446544	HEK293	kidney:	embryo
4	chr2:190446494-190446544	NT2-D1	testis:	n/a
5	chr2:190446494-190446544	HCT-116	colon:	n/a
6	chr2:190446494-190446544	RPTEC	kidney:	n/a
7	chr2:190446494-190446544	AG04450	lung:	fetal
8	chr2:190446494-190446544	MCF10A-Er-Src	breast:	n/a
9	chr2:190446494-190446544	HRCEpiC	kidney:	n/a
10	chr2:190446494-190446544	U87	brain:	n/a
11	chr2:190446494-190446544	K562	blood:	n/a
12	chr2:190446494-190446544	GM06990	blood:	n/a
13	chr2:190446494-190446544	ProgFib	skin:	n/a
14	chr2:190446494-190446544	ECC-1	luminal epithelium:	n/a
15	chr2:190446494-190446544	HCPEpiC	choroid plexus:	n/a
16	chr2:190446494-190446544	PANC-1	pancreas:	n/a
17	chr2:190446494-190446544	A549	lung:	n/a
18	chr2:190446494-190446544	SKMC	muscle:	n/a
19	chr2:190446494-190446544	BE2_C	brain:	n/a
20	chr2:190446494-190446544	AG09319	gingival:	n/a
21	chr2:190446494-190446544	Caco-2	colon:	n/a
22	chr2:190446494-190446544	GM12891	blood:	n/a
23	chr2:190446494-190446544	NH-A	brain:	n/a
24	chr2:190446494-190446544	MCF-7	breast:	n/a
25	chr2:190446494-190446544	AG10803	skin:	n/a
26	chr2:190446494-190446544	NHBE	bronchial:	n/a
27	chr2:190446494-190446544	SAEC	small airway:	n/a
28	chr2:190446494-190446544	CMK	blood:	n/a
29	chr2:190446494-190446544	Hela-S3	cervix:	n/a
30	chr2:190446494-190446544	HepG2	liver:	n/a
31	chr2:190446494-190446544	Jurkat	blood:	n/a
32	chr2:190446494-190446544	GM12878	blood:	n/a
33	chr2:190446494-190446544	PrEC	prostate:	n/a
34	chr2:190446494-190446544	AG04449	skin:	fetal
35	chr2:190446494-190446544	NHDF-neo	bronchial:	n/a
36	chr2:190446494-190446544	T-47D	breast:	n/a
37	chr2:190446494-190446544	GM12892	blood:	n/a
38	chr2:190446494-190446544	H1-hESC	embryonic stem cell:	embryo
39	chr2:190446494-190446544	ovcar-3	ovarian:	n/a
40	chr2:190446494-190446544	HCF	heart:	n/a
41	chr2:190446494-190446544	HUVEC	blood vessel:	n/a
42	chr2:190446494-190446544	HMEC	breast:	n/a
43	chr2:190446494-190446544	HNPCEpiC	eye:	n/a
44	chr2:190446494-190446544	IMR90	lung:	fetal
45	chr2:190446494-190446544	HCM	heart:	n/a
46	chr2:190446494-190446544	HL-60	blood:	n/a
47	chr2:190446494-190446544	Hepatocyte	liver:	n/a
48	chr2:190446494-190446544	GM19239	blood:	n/a
49	chr2:190446494-190446544	AG09309	skin:	n/a
50	chr2:190446494-190446544	AoSMC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190305660..190307734-chr2:190445889..190448100,2	K562	blood:
2	chr2:190443338..190447714-chr2:190524367..190527732,5	K562	blood:

Variant related genes	Relation type
SLC40A1	TF binding region
SLC40A1	CpG island
ENSG00000138381	Chromatin interaction
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10206897	0.88[EUR][1000 genomes]
rs10931425	0.85[EUR][1000 genomes]
rs12693542	0.90[CHB][hapmap]
rs1437883	0.91[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes]
rs1437884	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs17198990	0.85[EUR][1000 genomes]
rs17199004	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs17271183	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs34001547	0.85[EUR][1000 genomes]
rs6706281	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs6715669	0.85[EUR][1000 genomes]
rs6715900	0.85[EUR][1000 genomes]
rs6718933	0.84[EUR][1000 genomes]
rs6743001	0.85[EUR][1000 genomes]
rs71434664	0.84[EUR][1000 genomes]
rs7603186	0.84[CEU][hapmap];0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190442200-190446600	Active TSS	Right Atrium	heart
2	chr2:190443200-190446600	Active TSS	Brain Anterior Caudate	brain
3	chr2:190443200-190446600	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr2:190444000-190446600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr2:190444200-190446600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:190444400-190446600	Active TSS	Psoas Muscle	Psoas
7	chr2:190444400-190446800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr2:190444800-190446800	Active TSS	Fetal Kidney	kidney
9	chr2:190445000-190446600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr2:190445000-190447000	Active TSS	K562	blood
11	chr2:190445200-190446600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:190445400-190446800	Active TSS	Brain Cingulate Gyrus	brain
13	chr2:190445400-190447000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr2:190445800-190446600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:190445800-190446600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:190445800-190446600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
17	chr2:190446000-190446600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:190446000-190446600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr2:190446000-190446600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr2:190446000-190446600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:190446000-190446600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:190446000-190446600	Flanking Active TSS	Liver	Liver
23	chr2:190446000-190446600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr2:190446000-190446600	Flanking Active TSS	Placenta	Placenta
25	chr2:190446000-190446600	Flanking Active TSS	Thymus	Thymus
26	chr2:190446000-190446800	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr2:190446000-190446800	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr2:190446000-190446800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr2:190446000-190447000	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr2:190446000-190448200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:190446000-190449400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:190446200-190446600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr2:190446200-190446600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr2:190446200-190446600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:190446200-190446600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:190446200-190446600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
37	chr2:190446200-190446600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
38	chr2:190446200-190446600	Flanking Active TSS	Fetal Heart	heart
39	chr2:190446200-190446600	Flanking Active TSS	Fetal Stomach	stomach
40	chr2:190446200-190446600	Flanking Active TSS	Left Ventricle	heart
41	chr2:190446200-190446600	Flanking Active TSS	Lung	lung
42	chr2:190446200-190446600	Flanking Active TSS	Right Ventricle	heart
43	chr2:190446200-190446800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
44	chr2:190446200-190446800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:190446200-190446800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:190446200-190446800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
47	chr2:190446200-190446800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr2:190446200-190446800	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr2:190446200-190446800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr2:190446200-190446800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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