Variant report

Variant	rs2228084
Chromosome Location	chr1:45479709-45479710
allele	A/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:27)
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	RCOR1	chr1:45479611-45479778	K562	blood:	n/a	n/a
2	POLR2A	chr1:45477475-45482921	K562	blood:	n/a	n/a
3	CTCF	chr1:45479620-45479770	HCPEpiC	choroid plexus:	n/a	n/a
4	POLR2A	chr1:45477544-45479953	K562	blood:	n/a	n/a
5	SMC3	chr1:45479708-45480721	K562	blood:	n/a	n/a
6	NR2F2	chr1:45476833-45479943	K562	blood:	n/a	n/a
7	CTCF	chr1:45479680-45479830	AG10803	skin:	n/a	n/a
8	HEY1	chr1:45477581-45480785	K562	blood:	n/a	n/a
9	CTCF	chr1:45479620-45479770	AG09319	gingival:	n/a	n/a
10	CTCF	chr1:45479600-45479750	BJ	skin:	n/a	n/a
11	CTCF	chr1:45479186-45479751	T-47D	breast:	n/a	n/a
12	CTCF	chr1:45479680-45479830	GM12870	blood:	n/a	n/a
13	RAD21	chr1:45479569-45481167	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr1:45479319-45479883	HepG2	liver:	n/a	n/a
15	JUN	chr1:45476061-45480910	K562	blood:	n/a	chr1:45477407-45477414 chr1:45477406-45477414 chr1:45477191-45477203
16	POLR2A	chr1:45477763-45483536	K562	blood:	n/a	n/a
17	FOSL2	chr1:45479337-45479801	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:45477523-45480821	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:45305082..45310090-chr1:45475264..45482808,8	K562	blood:
2	chr1:45477030..45479805-chr1:46047527..46050763,5	K562	blood:
3	chr1:45475180..45477058-chr1:45478388..45480349,2	MCF-7	breast:
4	chr1:45193444..45198675-chr1:45475617..45480324,16	K562	blood:
5	chr1:45264279..45267905-chr1:45476139..45480748,9	K562	blood:
6	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
7	chr1:45476357..45485239-chr1:45761850..45773601,48	K562	blood:
8	chr1:45306981..45310503-chr1:45474976..45481200,7	K562	blood:
9	chr1:45449901..45454181-chr1:45475970..45480540,16	K562	blood:
10	chr1:45268954..45275189-chr1:45475024..45480055,7	K562	blood:
11	chr1:45476992..45480023-chr1:45798913..45801605,5	K562	blood:
12	chr1:45282320..45290015-chr1:45470338..45482903,45	K562	blood:
13	chr1:45284268..45287037-chr1:45476110..45479807,4	MCF-7	breast:
14	chr1:45194719..45198675-chr1:45474706..45481379,10	K562	blood:
15	chr1:45184334..45189303-chr1:45475138..45480545,18	K562	blood:
16	chr1:45478715..45481443-chr1:45824353..45825976,2	MCF-7	breast:
17	chr1:45283389..45288095-chr1:45474959..45480313,6	MCF-7	breast:
18	chr1:45240714..45243157-chr1:45476342..45480108,4	MCF-7	breast:
19	chr1:45281186..45291350-chr1:45463934..45483092,44	K562	blood:
20	chr1:45239592..45244618-chr1:45476667..45480609,10	K562	blood:
21	chr1:45205081..45206794-chr1:45478593..45481166,2	K562	blood:
22	chr1:45264355..45267553-chr1:45476139..45481796,8	K562	blood:
23	chr1:45184334..45189289-chr1:45475449..45480431,12	K562	blood:
24	chr1:45476853..45482658-chr1:45802506..45807966,11	K562	blood:
25	chr1:45264684..45267553-chr1:45478723..45482931,4	MCF-7	breast:
26	chr1:45478895..45481686-chr1:45791437..45793067,2	MCF-7	breast:
27	chr1:45476265..45486633-chr1:45761064..45774272,63	K562	blood:

No data

Variant related genes	Relation type
HECTD3	TF binding region
UROD	TF binding region
ENSG00000132780	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000186603	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000226499	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000238945	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000188396	Chromatin interaction
ENSG00000132781	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1144868	0.91[CHD][hapmap]
rs11548990	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12407565	0.82[ASW][hapmap]
rs1612575	0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs1969084	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs1995403	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs2202152	1.00[CHD][hapmap]
rs2234480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356302	0.91[CHD][hapmap]
rs238249	0.91[CHD][hapmap]
rs2997465	0.91[CHD][hapmap]
rs34134455	0.91[CHD][hapmap]
rs346689	0.85[JPT][hapmap]
rs346693	0.91[CHD][hapmap]
rs346696	0.91[CHD][hapmap]
rs346703	0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs346704	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs346706	0.86[CHD][hapmap]
rs346707	0.91[CHD][hapmap]
rs346711	0.85[JPT][hapmap]
rs346718	0.85[JPT][hapmap]
rs346720	0.85[JPT][hapmap]
rs346724	0.91[CHD][hapmap]
rs346725	0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs346732	0.91[CHD][hapmap]
rs346733	0.86[CHD][hapmap]
rs3850855	0.90[CHD][hapmap]
rs41312020	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454624	0.91[CHD][hapmap]
rs4660834	0.91[CHD][hapmap]
rs4660835	0.84[AMR][1000 genomes]
rs4660841	0.91[CHD][hapmap]
rs59432881	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6429556	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6664113	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6688318	0.91[CHD][hapmap]
rs6693885	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs72676543	0.81[EUR][1000 genomes]
rs72684406	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684412	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684416	0.98[EUR][1000 genomes]
rs72684425	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72684426	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72684447	0.84[AMR][1000 genomes]
rs7528534	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7529213	0.82[ASW][hapmap]
rs7543211	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45475600-45480400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:45477000-45480000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:45478400-45483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:45478600-45480600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:45478600-45482600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:45478600-45500000	Weak transcription	Aorta	Aorta
7	chr1:45478800-45479800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr1:45478800-45479800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:45478800-45480000	Weak transcription	Stomach Mucosa	stomach
10	chr1:45478800-45480200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:45478800-45480600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:45478800-45481400	Transcr. at gene 5' and 3'	K562	blood
13	chr1:45478800-45482200	Weak transcription	Psoas Muscle	Psoas
14	chr1:45478800-45482600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:45478800-45484000	Weak transcription	Right Atrium	heart
16	chr1:45479000-45479800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
17	chr1:45479000-45480000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:45479000-45480000	Weak transcription	Brain Substantia Nigra	brain
19	chr1:45479000-45480000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:45479000-45480200	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:45479000-45480200	Enhancers	Brain Germinal Matrix	brain
22	chr1:45479000-45480200	Genic enhancers	Fetal Intestine Small	intestine
23	chr1:45479000-45480400	Weak transcription	Fetal Brain Male	brain
24	chr1:45479000-45480400	Weak transcription	HSMMtube	muscle
25	chr1:45479000-45480400	Enhancers	Monocytes-CD14+_RO01746	blood
26	chr1:45479000-45480600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:45479000-45480600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:45479000-45480600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:45479000-45480600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:45479000-45480800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:45479000-45480800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:45479000-45480800	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr1:45479000-45480800	Genic enhancers	Fetal Muscle Leg	muscle
34	chr1:45479000-45480800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:45479000-45480800	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr1:45479000-45480800	Genic enhancers	NH-A	brain
37	chr1:45479000-45482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:45479000-45483400	Weak transcription	Primary B cells from cord blood	blood
39	chr1:45479000-45484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:45479000-45484200	Weak transcription	Esophagus	oesophagus
41	chr1:45479000-45485200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:45479000-45493000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:45479200-45479800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:45479200-45479800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:45479200-45479800	Weak transcription	Spleen	Spleen
46	chr1:45479200-45480000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:45479200-45480000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr1:45479200-45480000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:45479200-45480000	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:45479200-45480000	Genic enhancers	Duodenum Smooth Muscle	Duodenum

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