Variant report

Variant	rs4075681
Chromosome Location	chr12:50214637-50214638
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50210017..50215332-chr12:50220398..50225792,6	MCF-7	breast:
2	chr12:50213961..50216545-chr12:50234924..50237715,2	MCF-7	breast:
3	chr12:50200740..50202923-chr12:50213695..50216667,2	MCF-7	breast:
4	chr12:50168706..50170738-chr12:50213916..50216913,2	MCF-7	breast:
5	chr12:50200354..50203165-chr12:50213791..50216673,2	K562	blood:
6	chr12:50200354..50204251-chr12:50212561..50215291,3	K562	blood:

Variant related genes	Relation type
ENSG00000186666	Chromatin interaction
ENSG00000258057	Chromatin interaction
ENSG00000167566	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10875969	0.83[TSI][hapmap]
rs10875972	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169162	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs11169163	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611070	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11612227	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11836282	0.92[CEU][hapmap]
rs2603105	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2603112	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs2720291	0.82[TSI][hapmap]
rs2720293	0.88[CEU][hapmap]
rs2720298	0.83[TSI][hapmap]
rs2720301	0.88[EUR][1000 genomes]
rs2720302	0.81[EUR][1000 genomes]
rs59046026	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729281	0.83[TSI][hapmap]
rs73114127	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73114136	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73114137	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73114141	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7313563	0.87[CEU][hapmap]
rs751675	0.86[EUR][1000 genomes]
rs7953534	0.88[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7977000	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7978693	1.00[CEU][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4075681	PLEKHA9	cis	cerebellum	SCAN
rs4075681	CCDC65	cis	parietal	SCAN
rs4075681	RAPGEF3	cis	parietal	SCAN
rs4075681	ACVR1B	cis	cerebellum	SCAN
rs4075681	DBX2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50187200-50214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:50195200-50218400	Weak transcription	K562	blood
3	chr12:50197600-50220400	Weak transcription	A549	lung
4	chr12:50199400-50218400	Weak transcription	HMEC	breast
5	chr12:50199600-50214800	Weak transcription	Liver	Liver
6	chr12:50200000-50216800	Weak transcription	NHEK	skin
7	chr12:50200000-50219400	Weak transcription	Gastric	stomach
8	chr12:50200200-50214800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:50200400-50215000	Weak transcription	Dnd41	blood
10	chr12:50202200-50217000	Weak transcription	HepG2	liver
11	chr12:50202200-50218400	Weak transcription	Fetal Brain Female	brain
12	chr12:50203600-50218000	Weak transcription	NH-A	brain
13	chr12:50203600-50219800	Weak transcription	Aorta	Aorta
14	chr12:50203800-50215400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:50203800-50217800	Weak transcription	NHLF	lung
16	chr12:50203800-50218600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:50204200-50217800	Weak transcription	Fetal Brain Male	brain
18	chr12:50204400-50216600	Weak transcription	Brain Germinal Matrix	brain
19	chr12:50204400-50220200	Weak transcription	Fetal Kidney	kidney
20	chr12:50205000-50215000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:50205000-50215200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr12:50205200-50215000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:50205200-50215200	Weak transcription	Fetal Lung	lung
24	chr12:50205200-50219000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:50205200-50220000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:50205600-50215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:50205600-50216600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:50208800-50221200	Weak transcription	Small Intestine	intestine
29	chr12:50210000-50215200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:50210000-50215200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:50210200-50214800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:50210200-50214800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:50210200-50214800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:50210200-50214800	Weak transcription	Esophagus	oesophagus
35	chr12:50210200-50214800	Weak transcription	Spleen	Spleen
36	chr12:50210200-50215200	Weak transcription	Psoas Muscle	Psoas
37	chr12:50210200-50215600	Weak transcription	HSMM	muscle
38	chr12:50210200-50216600	Weak transcription	Ovary	ovary
39	chr12:50210200-50216800	Weak transcription	HSMMtube	muscle
40	chr12:50210200-50218000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:50210200-50218400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:50211600-50215800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:50212000-50217600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:50212200-50216000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:50212400-50214800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:50213200-50215200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:50213200-50215600	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr12:50213400-50216000	Enhancers	Adipose Nuclei	Adipose
49	chr12:50213600-50214800	Enhancers	GM12878-XiMat	blood
50	chr12:50213600-50214800	Enhancers	HUVEC	blood vessel

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