Variant report

Variant	rs2241877
Chromosome Location	chr2:234186489-234186490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234179437..234182271-chr2:234185909..234188121,2	MCF-7	breast:
2	chr2:234182703..234185905-chr2:234186252..234191203,5	K562	blood:
3	chr2:234157580..234161544-chr2:234185934..234189119,3	K562	blood:

Variant related genes	Relation type
ENSG00000252010	Chromatin interaction
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1045095	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10929033	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11685932	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs11894529	0.94[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13005285	0.95[CHB][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs1816753	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241876	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289475	0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35812841	0.81[ASN][1000 genomes]
rs3749079	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3792110	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4663136	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4663429	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6431259	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6431262	0.94[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6431270	0.90[ASN][1000 genomes]
rs6431655	0.85[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6431659	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs6705993	0.83[ASN][1000 genomes]
rs6717493	0.82[ASN][1000 genomes]
rs6737398	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs6754677	0.87[CHB][hapmap]
rs6861	0.94[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7587051	0.82[CHB][hapmap]
rs7587633	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7595748	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2241877	GIGYF2	cis	cerebellum	SCAN
rs2241877	SCARNA5	cis	parietal	SCAN
rs2241877	RFT1	trans	parietal	SCAN
rs2241877	ATG16L1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:234162400-234192000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:234162400-234196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:234162600-234188600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:234162600-234192400	Strong transcription	Osteobl	bone
9	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
11	chr2:234162800-234194000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:234162800-234197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:234163000-234192200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:234163000-234192200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:234163200-234188000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr2:234163200-234188800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:234163800-234188600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:234163800-234189000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr2:234164200-234205400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr2:234164200-234205400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:234164400-234192000	Strong transcription	NH-A	brain
24	chr2:234164400-234196800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:234164400-234197200	Strong transcription	Adipose Nuclei	Adipose
26	chr2:234164600-234190400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:234164600-234192000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:234164600-234192200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:234164600-234206000	Strong transcription	HepG2	liver
30	chr2:234164800-234195800	Strong transcription	Fetal Intestine Large	intestine
31	chr2:234165000-234192200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:234165000-234206000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:234165200-234205400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:234165400-234192000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr2:234166200-234191800	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr2:234166600-234189000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:234166800-234206000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:234169400-234197200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:234169800-234192000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:234171200-234191800	Strong transcription	HSMM	muscle
41	chr2:234172200-234204800	Strong transcription	Placenta	Placenta
42	chr2:234174000-234196000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:234176400-234187400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:234176800-234207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr2:234177000-234206000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:234177200-234192000	Strong transcription	HMEC	breast
47	chr2:234177200-234205400	Strong transcription	Dnd41	blood
48	chr2:234177600-234192000	Strong transcription	GM12878-XiMat	blood
49	chr2:234177800-234192200	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr2:234177800-234197200	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links