Variant report

Variant	rs2377671
Chromosome Location	chr12:9103842-9103843
allele	A/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	POLR2A	chr12:9103777-9103939	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr12:9101625-9103881	A549	lung:	n/a	chr12:9102284-9102297
3	CTCF	chr12:9101386-9103984	SK-N-SH	brain:	n/a	chr12:9102284-9102297
4	RAD21	chr12:9103576-9103919	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr12:9103780-9103930	BJ	skin:	n/a	n/a
6	IRF1	chr12:9103350-9103877	K562	blood:	n/a	chr12:9103658-9103671 chr12:9103656-9103670 chr12:9103660-9103671 chr12:9103659-9103676 chr12:9103658-9103671 chr12:9103660-9103670 chr12:9103658-9103671 chr12:9103661-9103672 chr12:9103761-9103774
7	ZNF384	chr12:9103552-9104030	K562	blood:	n/a	n/a
8	CTCF	chr12:9103700-9103850	HVMF	connective:	n/a	n/a
9	RCOR1	chr12:9103742-9103917	Hela-S3	cervix:	n/a	n/a
10	GATA2	chr12:9101382-9104014	SH-SY5Y	brain:	n/a	chr12:9101452-9101462 chr12:9101841-9101852
11	IRF1	chr12:9101572-9103880	K562	blood:	n/a	chr12:9103658-9103671 chr12:9103656-9103670 chr12:9103660-9103671 chr12:9103659-9103676 chr12:9103658-9103671 chr12:9103660-9103670 chr12:9103658-9103671 chr12:9103661-9103672 chr12:9103761-9103774 chr12:9102370-9102379 chr12:9102242-9102262
12	CTCF	chr12:9103553-9103890	GM12878	blood:	n/a	n/a
13	MXI1	chr12:9101035-9104283	SK-N-SH	brain:	n/a	chr12:9102579-9102588
14	CTCF	chr12:9103603-9103857	K562	blood:	n/a	n/a
15	GATA1	chr12:9101314-9103992	PBDE	blood:	n/a	chr12:9101452-9101462 chr12:9101841-9101852

No.	Distal block	Cell Line	Cell type
1	chr12:8850179..8851815-chr12:9101960..9104335,2	MCF-7	breast:
2	chr12:8831240..8834725-chr12:9101135..9103936,3	MCF-7	breast:
3	chr12:9103173..9107180-chr12:9112850..9116183,4	K562	blood:
4	chr12:9093611..9096195-chr12:9102368..9104030,2	K562	blood:
5	chr12:9097804..9100498-chr12:9103089..9104894,4	K562	blood:
6	chr12:8849018..8850959-chr12:9102785..9104647,2	K562	blood:
7	chr12:8849223..8851082-chr12:9101432..9104201,2	K562	blood:
8	chr12:9093100..9096905-chr12:9100746..9103868,4	K562	blood:
9	chr12:9103372..9104890-chr12:9110140..9112943,2	MCF-7	breast:
10	chr12:9103173..9105935-chr12:9114683..9116241,2	K562	blood:
11	chr12:9096830..9100498-chr12:9102068..9104762,4	K562	blood:

Variant related genes	Relation type
M6PR	TF binding region
ENSG00000166532	Chromatin interaction
ENSG00000256004	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10129061	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10400516	0.81[ASN][1000 genomes]
rs10743568	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771238	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11048190	0.84[ASN][1000 genomes]
rs11048195	0.84[ASN][1000 genomes]
rs11048264	0.81[ASN][1000 genomes]
rs11048337	0.83[ASN][1000 genomes]
rs11048338	0.83[ASN][1000 genomes]
rs11048344	0.83[ASN][1000 genomes]
rs11048345	0.83[ASN][1000 genomes]
rs1121401	0.85[ASN][1000 genomes]
rs11614202	0.88[ASN][1000 genomes]
rs12423746	0.83[ASN][1000 genomes]
rs12423817	0.83[ASN][1000 genomes]
rs12424026	0.83[ASN][1000 genomes]
rs12812913	0.83[ASN][1000 genomes]
rs12821842	0.83[ASN][1000 genomes]
rs12823100	0.83[ASN][1000 genomes]
rs12833375	0.83[ASN][1000 genomes]
rs1805248	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805724	0.84[ASN][1000 genomes]
rs1805725	0.88[ASN][1000 genomes]
rs1805727	0.87[ASN][1000 genomes]
rs1805735	0.81[ASN][1000 genomes]
rs1805754	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805761	0.80[ASN][1000 genomes]
rs2041624	0.83[ASN][1000 genomes]
rs2041625	0.83[ASN][1000 genomes]
rs2377672	0.82[ASN][1000 genomes]
rs2377673	0.83[ASN][1000 genomes]
rs2377674	0.83[ASN][1000 genomes]
rs2377676	0.85[ASN][1000 genomes]
rs34798934	0.83[ASN][1000 genomes]
rs4309200	0.83[ASN][1000 genomes]
rs4639983	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883203	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132930	0.83[ASN][1000 genomes]
rs7300767	0.83[ASN][1000 genomes]
rs7301381	0.81[ASN][1000 genomes]
rs7957321	0.83[ASN][1000 genomes]
rs7961355	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974486	0.85[ASN][1000 genomes]
rs933462	0.84[ASN][1000 genomes]
rs987917	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription 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	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2377671	M6PR	cis	lung	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9100400-9104000	Active TSS	GM12878-XiMat	blood
2	chr12:9101000-9104000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:9101000-9104400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:9101200-9104000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:9101200-9104000	Active TSS	A549	lung
6	chr12:9101600-9104000	Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr12:9101800-9104000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:9101800-9104600	Active TSS	Rectal Smooth Muscle	rectum
9	chr12:9102600-9104000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:9102800-9104000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr12:9102800-9104000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr12:9102800-9104200	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr12:9102800-9104200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:9102800-9105000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr12:9103000-9109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:9103200-9104800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr12:9103200-9105400	Weak transcription	Gastric	stomach
18	chr12:9103400-9104600	Flanking Active TSS	Dnd41	blood
19	chr12:9103400-9105600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:9103400-9112000	Weak transcription	Pancreas	Pancrea
21	chr12:9103400-9116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr12:9103600-9104000	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:9103600-9104000	Enhancers	Brain Germinal Matrix	brain
24	chr12:9103600-9104000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:9103600-9104000	Enhancers	Placenta	Placenta
26	chr12:9103600-9104000	Enhancers	Fetal Stomach	stomach
27	chr12:9103600-9104000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:9103600-9104000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:9103600-9104200	Enhancers	Colon Smooth Muscle	Colon
30	chr12:9103600-9104600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr12:9103600-9104800	Enhancers	Small Intestine	intestine
32	chr12:9103600-9105000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:9103600-9105000	Enhancers	Primary B cells from peripheral blood	blood
34	chr12:9103600-9105200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr12:9103600-9105200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:9103600-9105400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:9103600-9105400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:9103600-9105600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr12:9103600-9105600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr12:9103600-9105600	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:9103600-9105600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:9103600-9105600	Weak transcription	Fetal Intestine Small	intestine
43	chr12:9103600-9105800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:9103600-9110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:9103600-9114000	Weak transcription	Fetal Kidney	kidney
46	chr12:9103600-9114200	Weak transcription	Aorta	Aorta
47	chr12:9103600-9114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:9103600-9114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:9103800-9104000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:9103800-9104000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links