Variant report

Variant	rs2277326
Chromosome Location	chr12:58202419-58202420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58201131..58203130-chr2:73963168..73964881,2	MCF-7	breast:
2	chr12:58164894..58167465-chr12:58198689..58202991,3	K562	blood:
3	chr12:58201400..58203857-chr12:58230705..58233623,2	K562	blood:
4	chr12:58193274..58197647-chr12:58200040..58205215,7	MCF-7	breast:
5	chr12:58200080..58203835-chr12:58209165..58211460,3	K562	blood:
6	chr12:58196723..58199553-chr12:58199752..58203414,5	K562	blood:

Variant related genes	Relation type
ENSG00000144034	Chromatin interaction
ENSG00000270039	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000257953	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1050045	0.84[CEU][hapmap]
rs10877020	0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172337	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12368653	0.82[GIH][hapmap]
rs12371356	0.82[GIH][hapmap]
rs2270777	0.88[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs2307097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816896	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760340	0.84[JPT][hapmap]
rs7295422	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs7311632	0.83[GIH][hapmap]
rs7966795	0.85[MEX][hapmap]
rs799265	0.84[CEU][hapmap]
rs923828	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2277326	KIAA0748	cis	cerebellum	SCAN
rs2277326	RDH5	cis	parietal	SCAN
rs2277326	XRCC6BP1	cis	multi-tissue	Pritchard
rs2277326	DKFZP586D0919	cis	multi-tissue	Pritchard
rs2277326	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs2277326	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs2277326	TSFM	cis	lymphoblastoid	seeQTL
rs2277326	FAM119B	cis	cerebellum	SCAN
rs2277326	FAM119B	cis	lymphoblastoid	seeQTL
rs2277326	KRT75	cis	cerebellum	SCAN
rs2277326	KRT81	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:58178600-58207600	Strong transcription	Liver	Liver
3	chr12:58181400-58216000	Weak transcription	Fetal Brain Male	brain
4	chr12:58187000-58216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:58187200-58215600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:58188600-58207800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:58189000-58208400	Strong transcription	Fetal Stomach	stomach
8	chr12:58189200-58207800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:58189400-58207200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:58189800-58208400	Strong transcription	Placenta	Placenta
11	chr12:58190200-58216600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:58190400-58208000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:58190800-58215200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:58190800-58216200	Weak transcription	HUVEC	blood vessel
15	chr12:58191000-58216400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:58191200-58213600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:58191200-58216200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:58191600-58204200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:58191800-58204200	Weak transcription	HMEC	breast
20	chr12:58191800-58208400	Weak transcription	Psoas Muscle	Psoas
21	chr12:58192000-58210600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:58192200-58216200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:58192400-58205600	Strong transcription	Lung	lung
24	chr12:58193000-58210200	Strong transcription	Fetal Intestine Small	intestine
25	chr12:58193200-58215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:58193400-58216200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:58193800-58204200	Weak transcription	Stomach Mucosa	stomach
28	chr12:58194200-58215200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:58195200-58210600	Weak transcription	Small Intestine	intestine
30	chr12:58197000-58203000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:58197200-58211600	Weak transcription	A549	lung
32	chr12:58197200-58216400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:58197600-58203800	Weak transcription	K562	blood
34	chr12:58197600-58204000	Weak transcription	NHEK	skin
35	chr12:58197600-58206400	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr12:58197800-58208000	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:58198200-58203000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:58198200-58204400	Weak transcription	Hela-S3	cervix
39	chr12:58198200-58204600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:58198200-58207400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:58198400-58215000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:58199200-58207000	Strong transcription	Stomach Smooth Muscle	stomach
43	chr12:58199600-58205400	Strong transcription	Colon Smooth Muscle	Colon
44	chr12:58199800-58203400	Strong transcription	NH-A	brain
45	chr12:58199800-58203800	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr12:58199800-58205000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:58199800-58205000	Strong transcription	NHLF	lung
48	chr12:58199800-58205400	Strong transcription	Colonic Mucosa	Colon
49	chr12:58199800-58206800	Strong transcription	Brain Anterior Caudate	brain
50	chr12:58199800-58207200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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