Variant report

Variant	rs12144628
Chromosome Location	chr1:160509938-160509939
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160504989..160507235-chr1:160508336..160510301,3	K562	blood:
2	chr1:160502002..160504968-chr1:160508623..160511238,2	K562	blood:
3	chr1:160509002..160516145-chr1:160518936..160522666,8	K562	blood:
4	chr1:160504989..160508149-chr1:160508233..160510103,3	K562	blood:
5	chr1:160464006..160466333-chr1:160508326..160511280,2	K562	blood:
6	chr1:160509589..160511505-chr1:160535117..160536932,2	K562	blood:
7	chr1:160508215..160510935-chr1:160554435..160555982,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234425	Chromatin interaction
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1055880	0.80[CEU][hapmap]
rs1061217	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10752638	0.83[EUR][1000 genomes]
rs10797073	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10797083	0.82[EUR][1000 genomes]
rs10908789	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10908794	0.83[EUR][1000 genomes]
rs10908796	0.83[EUR][1000 genomes]
rs11265442	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11265452	0.84[CEU][hapmap]
rs1138323	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11583402	0.80[CEU][hapmap]
rs11585738	0.81[CEU][hapmap]
rs11590035	0.84[CEU][hapmap]
rs12402879	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12728784	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12736781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs151607	0.81[CEU][hapmap]
rs1572382	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1604783	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16832208	0.86[YRI][hapmap]
rs16832283	0.84[CEU][hapmap]
rs17381453	0.81[CEU][hapmap]
rs17385407	0.81[CEU][hapmap]
rs1809963	0.84[CEU][hapmap]
rs1998651	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2025516	0.88[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2025517	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2083128	0.88[CEU][hapmap]
rs2099604	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753260	0.84[CEU][hapmap]
rs3733264	0.81[CEU][hapmap]
rs3733265	0.81[CEU][hapmap]
rs3733266	0.81[CEU][hapmap]
rs3766387	0.84[CEU][hapmap]
rs3766388	0.85[CEU][hapmap]
rs3766389	0.81[CEU][hapmap]
rs3816146	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4106115	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5002947	0.84[CEU][hapmap]
rs6427535	0.83[EUR][1000 genomes]
rs6656191	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660233	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6668760	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6670721	0.84[CEU][hapmap]
rs6687641	0.84[CEU][hapmap]
rs6692382	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7515302	0.91[ASN][1000 genomes]
rs7528976	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534679	0.85[EUR][1000 genomes]
rs7547054	0.84[CEU][hapmap]
rs7550771	0.84[CEU][hapmap]
rs912582	0.81[CEU][hapmap]
rs9726326	0.85[EUR][1000 genomes]
rs977019	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12144628	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160506200-160511400	Weak transcription	Small Intestine	intestine
2	chr1:160507600-160515400	Enhancers	Fetal Intestine Large	intestine
3	chr1:160507800-160515400	Enhancers	Fetal Intestine Small	intestine
4	chr1:160508400-160510000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:160508400-160511800	Enhancers	Pancreas	Pancrea
6	chr1:160508400-160512000	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:160508400-160512000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:160508400-160512600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr1:160508400-160513200	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:160508600-160510000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:160508600-160510000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:160508600-160510000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:160508600-160510200	Flanking Active TSS	HepG2	liver
14	chr1:160508600-160510600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:160508600-160510800	Flanking Active TSS	Dnd41	blood
16	chr1:160508600-160512200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:160508600-160513200	Enhancers	Liver	Liver
18	chr1:160508800-160510000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr1:160508800-160510200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:160508800-160510600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:160508800-160510800	Flanking Active TSS	GM12878-XiMat	blood
22	chr1:160508800-160512800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:160509000-160510000	Flanking Active TSS	K562	blood
24	chr1:160509000-160510400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr1:160509000-160510600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:160509000-160510800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:160509200-160510000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:160509400-160510000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:160509400-160510600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr1:160509400-160511600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:160509400-160512000	Weak transcription	HMEC	breast
32	chr1:160509400-160512000	Weak transcription	NHEK	skin
33	chr1:160509600-160510000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:160509600-160510000	Enhancers	Right Atrium	heart
35	chr1:160509600-160510200	Enhancers	Left Ventricle	heart
36	chr1:160509600-160510600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr1:160509600-160510600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:160509600-160510600	Flanking Active TSS	Fetal Thymus	thymus
39	chr1:160509600-160510800	Flanking Active TSS	Thymus	Thymus
40	chr1:160509600-160512200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:160509800-160510000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr1:160509800-160510200	Flanking Active TSS	Stomach Mucosa	stomach
43	chr1:160509800-160510400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr1:160509800-160510600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr1:160509800-160510600	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr1:160509800-160510600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr1:160509800-160510600	Weak transcription	Colonic Mucosa	Colon
48	chr1:160509800-160510800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr1:160509800-160510800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr1:160509800-160511000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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