Variant report

Variant	rs968850
Chromosome Location	chr2:58273009-58273010
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	MTA3	chr2:58272784-58275064	GM12878	blood:	n/a	n/a
2	MAFF	chr2:58272265-58273010	K562	blood:	n/a	n/a
3	POLR2A	chr2:58272790-58275637	GM19099	blood:	n/a	n/a
4	UBTF	chr2:58272913-58275030	K562	blood:	n/a	n/a
5	POLR2A	chr2:58272024-58275047	GM18951	blood:	n/a	n/a
6	POLR2A	chr2:58271963-58275203	GM19193	blood:	n/a	n/a
7	POLR2A	chr2:58272795-58274822	GM12892	blood:	n/a	n/a
8	POLR2A	chr2:58272171-58275631	GM18505	blood:	n/a	n/a
9	GATA1	chr2:58272870-58275670	PBDE	blood:	n/a	n/a
10	POLR2A	chr2:58272761-58274999	GM18526	blood:	n/a	n/a
11	POLR2A	chr2:58272724-58275051	GM12892	blood:	n/a	n/a
12	POU2F2	chr2:58272939-58273320	GM12891	blood:	n/a	n/a
13	CHD1	chr2:58271698-58275822	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:58272897-58274697	GM12891	blood:	n/a	n/a
15	POLR2A	chr2:58272914-58274707	K562	blood:	n/a	n/a
16	POLR2A	chr2:58272868-58274881	GM15510	blood:	n/a	n/a
17	POLR2A	chr2:58272739-58275038	GM12878	blood:	n/a	n/a
18	RUNX3	chr2:58272658-58273161	GM12878	blood:	n/a	n/a
19	E2F6	chr2:58272908-58273081	K562	blood:	n/a	n/a
20	POLR2A	chr2:58273002-58275470	K562	blood:	n/a	n/a
21	POLR2A	chr2:58272798-58274789	GM12891	blood:	n/a	n/a
22	POLR2A	chr2:58272929-58273137	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:58272668-58274786	GM12892	blood:	n/a	n/a
24	POLR2A	chr2:58272698-58275023	GM12892	blood:	n/a	n/a
25	POLR2A	chr2:58271253-58275620	GM12891	blood:	n/a	n/a
26	POLR2A	chr2:58271753-58275667	GM12878	blood:	n/a	n/a
27	TBP	chr2:58272185-58273059	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:58272746-58273143	GM12891	blood:	n/a	n/a
29	POLR2A	chr2:58271686-58275020	GM12878	blood:	n/a	n/a
30	NFATC1	chr2:58272587-58274715	GM12878	blood:	n/a	n/a
31	MAFK	chr2:58272770-58273071	HepG2	liver:	n/a	chr2:58272902-58272916 chr2:58272904-58272915 chr2:58272903-58272918 chr2:58272903-58272919
32	MAFF	chr2:58272812-58273078	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:58133863..58138456-chr2:58272095..58275151,4	MCF-7	breast:
2	chr2:58133060..58135151-chr2:58272508..58275235,2	MCF-7	breast:
3	chr2:58258901..58260862-chr2:58271685..58273683,2	K562	blood:
4	chr2:58272245..58275889-chr2:58464232..58469335,5	K562	blood:

Variant related genes	Relation type
VRK2	TF binding region
ENSG00000115392	Chromatin interaction
ENSG00000273063	Chromatin interaction
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10188390	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10210198	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10496086	0.91[EUR][1000 genomes]
rs10496087	0.91[EUR][1000 genomes]
rs1078191	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11898024	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12465171	0.92[EUR][1000 genomes]
rs12467842	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12469522	0.84[EUR][1000 genomes]
rs12470851	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12471043	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12473840	0.84[EUR][1000 genomes]
rs12478718	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13386389	0.86[EUR][1000 genomes]
rs1371212	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1518403	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17049308	0.84[ASN][1000 genomes]
rs17049312	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17049314	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17049316	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17049321	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17830749	0.94[EUR][1000 genomes]
rs2118897	0.91[EUR][1000 genomes]
rs34191187	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35876471	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3771203	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55856965	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61548822	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6732965	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67484511	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72810305	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72810306	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72810307	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72810308	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72810316	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72810317	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72810318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72810320	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72810323	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72810325	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72810332	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72810334	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72810337	0.85[EUR][1000 genomes]
rs728574	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834159	chr2:58101262-58283655	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv999591	chr2:58214871-58316147	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv582097	chr2:58266099-58346966	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv874201	chr2:58269871-58350504	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv874202	chr2:58269871-58375688	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58260400-58273400	Weak transcription	Ovary	ovary
2	chr2:58266600-58273200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:58266800-58273400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:58268000-58273200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:58268600-58273400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:58269200-58273400	Weak transcription	Gastric	stomach
7	chr2:58270000-58273400	Weak transcription	Fetal Brain Male	brain
8	chr2:58270200-58273200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:58270400-58273200	Weak transcription	NH-A	brain
10	chr2:58271600-58273200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:58271600-58273400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:58271800-58273200	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:58271800-58273200	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:58271800-58273200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:58271800-58273200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:58271800-58273400	Enhancers	Left Ventricle	heart
17	chr2:58272000-58273200	Enhancers	Primary T cells from cord blood	blood
18	chr2:58272000-58273200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:58272200-58273200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:58272200-58273200	Enhancers	Fetal Heart	heart
21	chr2:58272200-58273200	Enhancers	NHDF-Ad	bronchial
22	chr2:58272200-58273600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr2:58272200-58275600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:58272400-58273200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:58272400-58273200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr2:58272400-58273200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:58272400-58273200	Enhancers	Brain Angular Gyrus	brain
28	chr2:58272400-58273200	Weak transcription	Brain Substantia Nigra	brain
29	chr2:58272400-58273200	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr2:58272400-58273200	Enhancers	NHLF	lung
31	chr2:58272400-58273400	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr2:58272400-58273600	Flanking Active TSS	Dnd41	blood
33	chr2:58272400-58275200	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr2:58272600-58273200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr2:58272600-58273400	Weak transcription	Small Intestine	intestine
36	chr2:58272600-58273400	Weak transcription	Spleen	Spleen
37	chr2:58272600-58273600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:58272600-58275400	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr2:58272600-58275800	Active TSS	K562	blood
40	chr2:58272600-58277400	Active TSS	GM12878-XiMat	blood
41	chr2:58272800-58273200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:58272800-58273200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:58272800-58273200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr2:58272800-58273200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:58272800-58273200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:58272800-58273200	Active TSS	Brain Hippocampus Middle	brain
47	chr2:58272800-58273200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:58272800-58273200	Enhancers	Fetal Thymus	thymus
49	chr2:58272800-58273200	Enhancers	Osteobl	bone
50	chr2:58272800-58273400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links