Variant report

Variant	rs12139524
Chromosome Location	chr1:161698660-161698661
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161591405..161593904-chr1:161697560..161699954,2	K562	blood:
2	chr1:161696482..161699035-chr1:161718061..161722028,6	K562	blood:
3	chr1:161657417..161659539-chr1:161696325..161698709,3	K562	blood:
4	chr1:161696672..161698764-chr1:161719597..161721628,3	K562	blood:
5	chr1:161654373..161658306-chr1:161696464..161699587,3	MCF-7	breast:
6	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
7	chr1:161651291..161653505-chr1:161696476..161699114,3	K562	blood:
8	chr1:161697451..161700405-chr1:161734526..161737492,2	K562	blood:
9	chr1:161640986..161643411-chr1:161696404..161699095,2	MCF-7	breast:
10	chr1:161645664..161648632-chr1:161696817..161700044,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213075	Chromatin interaction
ENSG00000081721	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000226889	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10799932	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10917810	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576107	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585450	0.89[AMR][1000 genomes]
rs12136661	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503810	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503811	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847382	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1875763	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6686408	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6686535	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv516773	chr1:161691433-161702763	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
6	nsv464195	chr1:161693003-161702792	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
7	nsv548076	chr1:161693003-161702792	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12139524	FCRLA	cis	multi-tissue	Pritchard
rs12139524	FCRLA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161697600-161699600	Weak transcription	Hela-S3	cervix
2	chr1:161697600-161700200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:161697600-161700200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:161697600-161700200	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr1:161697600-161700800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:161697600-161700800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:161697600-161700800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:161697800-161698800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:161697800-161698800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:161697800-161699200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:161697800-161699400	Weak transcription	HUVEC	blood vessel
12	chr1:161697800-161700000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:161697800-161700000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:161697800-161700000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:161697800-161700000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:161697800-161700600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:161697800-161700600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:161697800-161700800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:161697800-161700800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:161697800-161700800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:161697800-161700800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:161697800-161706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:161698000-161699200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:161698000-161699200	Weak transcription	HMEC	breast
25	chr1:161698000-161699600	Weak transcription	HSMM	muscle
26	chr1:161698000-161699800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:161698000-161700000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:161698000-161700000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:161698000-161700000	Weak transcription	NH-A	brain
30	chr1:161698000-161700000	Weak transcription	NHLF	lung
31	chr1:161698000-161700000	Weak transcription	Osteobl	bone
32	chr1:161698000-161700400	Weak transcription	Primary B cells from cord blood	blood
33	chr1:161698000-161700600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:161698000-161702600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:161698000-161703400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:161698000-161703400	Enhancers	K562	blood
37	chr1:161698000-161706000	Enhancers	NHEK	skin
38	chr1:161698000-161707600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:161698200-161700400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:161698400-161698800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:161698400-161699200	Flanking Active TSS	GM12878-XiMat	blood
42	chr1:161698400-161700400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
43	chr1:161698400-161700600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:161698400-161704400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:161698600-161698800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
46	chr1:161698600-161698800	Bivalent Enhancer	Primary T cells from cord blood	blood
47	chr1:161698600-161698800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:161698600-161698800	Enhancers	Right Ventricle	heart
49	chr1:161698600-161699000	Bivalent Enhancer	Dnd41	blood
50	chr1:161698600-161700200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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