Variant report

Variant	rs12727170
Chromosome Location	chr1:151832901-151832902
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151819170..151821882-chr1:151830861..151833145,2	K562	blood:
2	chr1:151823384..151829926-chr1:151830365..151837191,11	MCF-7	breast:
3	chr1:151831282..151833354-chr1:151964216..151966814,2	K562	blood:
4	chr1:151831860..151834809-chr1:151847817..151849613,2	MCF-7	breast:
5	chr1:151832360..151835660-chr1:151836036..151839920,4	MCF-7	breast:
6	chr1:151832485..151835043-chr1:151841039..151843402,2	MCF-7	breast:
7	chr1:151818078..151821727-chr1:151829199..151833455,4	MCF-7	breast:
8	chr1:151821929..151826041-chr1:151829913..151833427,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196407	Chromatin interaction
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10888445	0.81[CHB][hapmap]
rs1129117	0.81[ASN][1000 genomes]
rs12567049	0.81[ASN][1000 genomes]
rs16833604	0.81[ASN][1000 genomes]
rs2279503	0.84[CHD][hapmap]
rs2879130	0.97[CHD][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs6587625	0.90[CHD][hapmap]
rs7523082	0.80[CHB][hapmap]
rs7556386	0.85[CHD][hapmap]
rs923547	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3390723	chr1:151832128-151836426	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12727170	LINGO4	cis	cerebellum	SCAN
rs12727170	LCE2C	cis	cerebellum	SCAN
rs12727170	OTUD7B	cis	cerebellum	SCAN
rs12727170	SELENBP1	cis	parietal	SCAN
rs12727170	THEM4	cis	lymphoblastoid	seeQTL
rs12727170	SPRR2G	cis	parietal	SCAN
rs12727170	S100A10	cis	lymphoblastoid	seeQTL
rs12727170	CTSK	cis	cerebellum	SCAN
rs12727170	C1orf68	cis	cerebellum	SCAN
rs12727170	PGLYRP3	cis	parietal	SCAN
rs12727170	S100A10	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151819200-151847600	Weak transcription	Thymus	Thymus
2	chr1:151821600-151845600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:151826400-151846200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151827600-151839800	Weak transcription	Hela-S3	cervix
5	chr1:151828200-151835400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:151828800-151837000	Weak transcription	Right Ventricle	heart
7	chr1:151829000-151845200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:151829400-151834200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:151830000-151833400	Enhancers	HMEC	breast
10	chr1:151830000-151833600	Enhancers	NHEK	skin
11	chr1:151830000-151833800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:151830600-151834400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:151831000-151834000	Enhancers	Esophagus	oesophagus
14	chr1:151831000-151881400	Weak transcription	Ovary	ovary
15	chr1:151831200-151835000	Enhancers	Placenta	Placenta
16	chr1:151831600-151834200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:151831800-151834000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:151832000-151833000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:151832000-151833400	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:151832000-151859600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:151832200-151833400	Enhancers	GM12878-XiMat	blood
22	chr1:151832200-151834000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
23	chr1:151832200-151834400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr1:151832400-151833800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr1:151832400-151834400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr1:151832600-151833200	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
27	chr1:151832600-151833400	Weak transcription	Fetal Thymus	thymus
28	chr1:151832600-151834000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr1:151832600-151834200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:151832600-151834400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
31	chr1:151832800-151833000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:151832800-151833000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
33	chr1:151832800-151833200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
34	chr1:151832800-151833200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
35	chr1:151832800-151833200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:151832800-151833400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr1:151832800-151834200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:151832800-151840000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:151832800-151846000	Weak transcription	Spleen	Spleen

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