Variant report

Variant	rs12977469
Chromosome Location	chr19:39126734-39126735
allele	A/G
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39033468..39036345-chr19:39125493..39127888,3	K562	blood:
2	chr19:39124852..39127091-chr19:39168674..39171313,2	K562	blood:
3	chr19:39125520..39127850-chr19:39138032..39139918,2	K562	blood:
4	chr19:39107787..39109799-chr19:39125420..39127051,2	MCF-7	breast:
5	chr19:39033384..39036751-chr19:39123967..39127917,4	K562	blood:
6	chr19:39125533..39130601-chr19:39201644..39207054,6	MCF-7	breast:
7	chr19:39126407..39129417-chr19:39138116..39140606,3	MCF-7	breast:
8	chr19:39033772..39036275-chr19:39124908..39126988,2	MCF-7	breast:
9	chr19:39126238..39128898-chr19:39190173..39192471,2	K562	blood:
10	chr19:39113554..39117374-chr19:39123915..39127746,4	MCF-7	breast:
11	chr19:39125934..39129387-chr19:39129539..39132887,4	MCF-7	breast:
12	chr19:39126429..39128678-chr19:39138239..39140432,2	K562	blood:
13	chr19:39106811..39110494-chr19:39123822..39128125,5	K562	blood:
14	chr19:39126147..39129376-chr19:39327269..39331362,4	MCF-7	breast:
15	chr19:39126170..39130709-chr19:39210922..39213805,4	MCF-7	breast:
16	chr19:39125626..39127336-chr19:39202058..39204269,2	K562	blood:
17	chr19:38892716..38897062-chr19:39125285..39127901,4	K562	blood:
18	chr19:39112082..39114534-chr19:39125989..39129017,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130244	Chromatin interaction
ENSG00000130402	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000178982	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10445564	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12976749	0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs13345885	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs1862371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978443	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs2232992	0.87[CEU][hapmap];0.92[TSI][hapmap]
rs2287732	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs2287733	1.00[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs3786834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4592774	0.80[EUR][1000 genomes]
rs62120358	0.88[EUR][1000 genomes]
rs7251456	0.81[CEU][hapmap]
rs750438	0.94[ASW][hapmap];0.94[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs888994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9304576	0.81[CHB][hapmap]

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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12977469	GSK3A	cis	cerebellum	SCAN
rs12977469	PLAUR	cis	cerebellum	SCAN
rs12977469	LYPD4	cis	parietal	SCAN
rs12977469	ZFP36	cis	parietal	SCAN
rs12977469	SELV	cis	parietal	SCAN
rs12977469	AP2S1	cis	cerebellum	SCAN
rs12977469	TMEM145	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39111000-39127000	Strong transcription	Thymus	Thymus
2	chr19:39111000-39127400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr19:39111000-39128800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr19:39111200-39127600	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr19:39111200-39127600	Strong transcription	Brain Anterior Caudate	brain
6	chr19:39111200-39130400	Strong transcription	Stomach Smooth Muscle	stomach
7	chr19:39111200-39130800	Strong transcription	Fetal Stomach	stomach
8	chr19:39111200-39131000	Weak transcription	Right Atrium	heart
9	chr19:39111800-39127200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr19:39115600-39127200	Weak transcription	NHDF-Ad	bronchial
11	chr19:39120600-39127400	Weak transcription	NH-A	brain
12	chr19:39120800-39137800	Weak transcription	Fetal Brain Male	brain
13	chr19:39121600-39132400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:39123000-39127400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:39123800-39127200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:39123800-39132600	Weak transcription	Gastric	stomach
17	chr19:39123800-39137800	Weak transcription	Ovary	ovary
18	chr19:39125200-39127000	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr19:39125200-39127000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr19:39125200-39127000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:39125200-39127600	Genic enhancers	GM12878-XiMat	blood
22	chr19:39125200-39127800	Genic enhancers	A549	lung
23	chr19:39125200-39128000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:39125200-39128200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr19:39125400-39126800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr19:39125400-39126800	Genic enhancers	Esophagus	oesophagus
27	chr19:39125400-39126800	Genic enhancers	HMEC	breast
28	chr19:39125400-39127200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:39125400-39127200	Genic enhancers	Fetal Intestine Large	intestine
30	chr19:39125400-39127400	Genic enhancers	Primary B cells from peripheral blood	blood
31	chr19:39125400-39127400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:39125400-39127600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:39125400-39127800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
34	chr19:39125400-39127800	Genic enhancers	Left Ventricle	heart
35	chr19:39125400-39128000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:39125400-39128000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr19:39125400-39128000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:39125400-39128000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:39125400-39128000	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr19:39125400-39128000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr19:39125400-39128400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr19:39125400-39128400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:39125400-39128400	Genic enhancers	Fetal Intestine Small	intestine
44	chr19:39125400-39128400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
45	chr19:39125400-39128400	Genic enhancers	NHEK	skin
46	chr19:39125400-39128800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:39125400-39129600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:39125600-39126800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:39125600-39126800	Strong transcription	Fetal Lung	lung
50	chr19:39125600-39127000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links