Variant report

Variant	rs12214669
Chromosome Location	chr6:33556605-33556606
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33555689..33557372-chr6:33575674..33577429,2	MCF-7	breast:
2	chr6:33555453..33558278-chr6:33607870..33609566,2	K562	blood:
3	chr6:33556084..33559190-chr6:33561463..33564085,3	K562	blood:
4	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:
5	chr6:33554633..33558061-chr6:33675915..33678804,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10947418	0.86[AFR][1000 genomes]
rs10947432	1.00[LWK][hapmap]
rs11755257	0.86[AFR][1000 genomes]
rs11757379	0.82[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes]
rs11757612	0.86[AFR][1000 genomes]
rs11758330	0.86[AFR][1000 genomes]
rs12189725	1.00[LWK][hapmap]
rs12200154	0.86[AFR][1000 genomes]
rs12203688	1.00[LWK][hapmap]
rs12211490	1.00[LWK][hapmap]
rs12214476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195171	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13204162	1.00[LWK][hapmap]
rs13214874	1.00[LWK][hapmap]
rs13219209	0.90[EUR][1000 genomes]
rs17627049	0.85[CHD][hapmap]
rs2227925	0.86[AFR][1000 genomes]
rs3818532	1.00[LWK][hapmap]
rs4559081	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];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909950	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs71565391	0.80[EUR][1000 genomes]
rs71565393	0.86[AFR][1000 genomes]
rs877187	1.00[LWK][hapmap]

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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12214669	ITPR3	cis	multi-tissue	Pritchard
rs12214669	LEMD2	cis	parietal	SCAN
rs12214669	C6orf125	cis	cerebellum	SCAN
rs12214669	FKBP5	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33548400-33557000	Weak transcription	HSMM	muscle
2	chr6:33548400-33557200	Weak transcription	NHDF-Ad	bronchial
3	chr6:33548400-33557600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:33548400-33557800	Weak transcription	Right Atrium	heart
5	chr6:33548600-33560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:33548800-33557800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:33551800-33557200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:33552000-33557000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:33553600-33557000	Weak transcription	Ovary	ovary
10	chr6:33553600-33558000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:33553800-33556800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:33553800-33556800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:33553800-33556800	Weak transcription	Stomach Mucosa	stomach
14	chr6:33553800-33557000	Weak transcription	Fetal Stomach	stomach
15	chr6:33553800-33557000	Weak transcription	HMEC	breast
16	chr6:33553800-33557000	Weak transcription	HSMMtube	muscle
17	chr6:33553800-33557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:33553800-33557200	Weak transcription	Fetal Heart	heart
19	chr6:33553800-33557400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:33553800-33557400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr6:33553800-33557600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:33553800-33557600	Weak transcription	Left Ventricle	heart
23	chr6:33553800-33557600	Weak transcription	NH-A	brain
24	chr6:33553800-33557600	Weak transcription	Osteobl	bone
25	chr6:33553800-33557800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:33553800-33557800	Weak transcription	Esophagus	oesophagus
27	chr6:33553800-33558400	Weak transcription	Gastric	stomach
28	chr6:33553800-33560400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:33554000-33557000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:33554000-33557000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr6:33554000-33557000	Weak transcription	Adipose Nuclei	Adipose
32	chr6:33554000-33557000	Weak transcription	Fetal Lung	lung
33	chr6:33554000-33557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:33554000-33557200	Weak transcription	Placenta	Placenta
35	chr6:33554000-33557200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:33554000-33557400	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:33554000-33557600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:33554000-33557600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:33554000-33557600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:33554000-33557600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:33554000-33557600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:33554000-33557800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:33554000-33557800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr6:33554000-33557800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:33554000-33558400	Weak transcription	Fetal Kidney	kidney
46	chr6:33554000-33560400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:33554000-33560400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:33554000-33560600	Weak transcription	Brain Angular Gyrus	brain
49	chr6:33554000-33560800	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:33554200-33556800	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links